Genetic alterations in isocitrate dehydrogenase and other genes in malignant glioma

ABSTRACT

We found mutations of the R132 residue of isocitrate dehydrogenase 1 (IDH1) in the majority of grade II and III astrocytomas and oligodendrogliomas as well as in gliblastomas that develop from these lower grade lesions. Those tumors without mutations in IDH1 often had mutations at the analogous R172 residue of the closely related IDH2 gene. These findings have important implications for the pathogenesis and diagnosis of malignant gliomas.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.15/928,811, filed Mar. 22, 2018, which is a continuation of U.S.application Ser. No. 15/353,002, filed Nov. 16, 2016, which is adivisional of U.S. application Ser. No. 14/102,730 filed Dec. 11, 2013,which is a continuation of U.S. application Ser. No. 13/412,696, filedMar. 6, 2012; which is a continuation of U.S. application Ser. No.13/060,191, filed Jun. 7, 2011; which is a 371 application ofInternational Application No. PCT/US2009/055803, filed Sep. 3, 2009;which claims benefit of U.S. Application No. 61/093,739, filed Sep. 3,2008; U.S. Application No. 61/110,397, filed Oct. 31, 2008 and U.S.Application No. 61/162,737, filed Mar. 24, 2009. The contents of each ofthese applications are incorporated herein by reference in theirentirety.

GOVERNMENT SUPPORT

This invention was made with government support under CA 43460, CA57345, CA 62924, R01CA118822, NS20023-21, R37CA11898-34, and CA 121113awarded by the National Institutes of Health. The government has certainrights in the invention.

TECHNICAL FIELD OF THE INVENTION

This invention is related to the area of cancer diagnostics,prognostics, drug screening, and therapeutics. In particular, it relatesto brain tumors in general, and glioblastoma multiforme, in particular.

BACKGROUND OF THE INVENTION

Gliomas, the most common type of primary brain tumors, are classified asGrade I to Grade IV using histopathological and clinical criteriaestablished by the World Health Organization (WHO)¹. This group oftumors includes a number of specific histologies, the most common ofwhich are astrocytomas, oligodendrogliomas, and ependymomas. Grade Igliomas, often considered to be benign lesions, are generally curablewith complete surgical resection and rarely, if ever, evolve intohigher-grade lesions². However, tumors of Grades II and III aremalignant tumors that grow invasively, progress to higher-grade lesions,and carry a correspondingly poor prognosis. Grade IV tumors(glioblastoma multiforme, GBM) are the most invasive form and have adismal prognosis^(3, 4). Using histopathologic criteria, it isimpossible to distinguish a secondary GBM, defined as one which occursin a patient previously diagnosed with a lower grade glioma, from aprimary GBM which has no known antecedent tumor^(5, 6).

A number of genes are known to be genetically altered in gliomas,including TP53, PTEN, CDKN2A, and EGFR⁷⁻¹². These alterations tend tooccur in a defined order in the progression to high grade tumors. TP53mutation appears to be a relatively early event during astrocytomadevelopment, while loss or mutation of PTEN and amplification of EGFRare characteristic of higher-grade tumors^(6,13,14). Inoligodendrogliomas, allelic losses of 1p and 19q occur in many Grade IItumors while losses of 9p21 are largely confined to Grade III tumors¹⁵.

There is a continuing need in the art to identify the causes,identifiers, and remedies for glioblastomas and other brain tumors.

SUMMARY OF THE INVENTION

According to one aspect of the invention a method is provided ofcharacterizing a glioblastoma multiforme (GBM) tumor in a human subject.A GBM tumor is analyzed to identify the presence or absence of a somaticmutation at codon 132 in isocitrate dehydrogenase 1 (IDH1) or at codon172 in isocitrate dehydrogenase 2 (IDH2) in a GBM tumor of a humansubject.

Also provided as another aspect of the invention is an isolated antibodywhich specifically binds R132H IDH1, or R132C IDH1, or R132S IDH1, orR132L IDH1, or R132G IDH1, but not R132 IDH1; or R172M IDH2, R172G IDH2,or R172K IDH2, but not R172; i.e., mutant forms of IDH1 or IDH2 whichare found in GBM. Also provided is an isolated antibody whichspecifically binds R132 IDH1 or R172 IDH2, i.e., wild-type active sitesof IDH1 or IDH2.

Another aspect of the invention is a method of immunizing a mammal. AnIDH1 mutant polypolypeptide comprising at least 8 contiguous amino acidresidues of a human IDH1 protein or an IDH2 mutant polypolypeptidecomprising at least 8 contiguous amino acid residues of a human IDH2protein found in a human tumor is administered to a mammal. The at least8 contiguous amino acid residues comprise residue 132 or IDH1 or residue172 of IDH2. Residue 132 or residue 172 is not arginine. Antibodiesand/or T cells which are immunoreactive with epitopes found on the IDH1or IDH2 mutant polypeptide but not found on normal IDH1 or IDH2 areproduced.

Also provided as another aspect of the invention is an IDH1 or IDH2mutant polypeptide comprising at least 8 but less than 200 contiguousamino acid residues of a human IDH1 or IDH2 protein found in a humantumor. The at least 8 contiguous amino acid residues comprise residue132 of IDH1 or residue 172 of IDH2. Residues 132 or 172 are not R.

An additional aspect of the invention is an isolated polynucleotidecomprising at least 18 but less than 600 contiguous nucleotide residuesof a coding sequence of a human IDH1 or human IDH2 protein found in ahuman tumor. The at least 18 contiguous amino acid residues comprisenucleotides 394 and/or 395 of IDH1 or nucleotide 515 or IDH2.Nucleotides 394 and/or 395 of IDH1 are not C and/or G, respectively.Residue 515 of IDH2 is not G.

Another aspect of the invention is a method of immunizing a mammal. AnIDH1 polypeptide comprising at least 8 contiguous amino acid residues ofa human IDH1 protein or an IDH2 polypeptide comprising at least 8contiguous amino acid residues of a human IDH2 protein is administeredto a mammal. The at least 8 contiguous amino acid residues compriseresidue 132 of IDH1 or residue 172 of IDH2. Residue 132 or residue 172is arginine. Antibodies and/or T cells which are immunoreactive withepitopes found on the IDH1 or IDH2 polypeptide are produced.

Also provided as another aspect of the invention is an IDH1 or IDH2polypeptide comprising at least 8 but less than 200 contiguous aminoacid residues of a human IDH1 or IDH2 protein. The at least 8 contiguousamino acid residues comprise residue 132 of IDH1 or residue 172 of IDH2.Residues 132 or 172 are R.

Still another aspect of the invention is a method of detecting ordiagnosing glioblastoma multiforme (GBM) or minimal residual disease ofGBM or molecular relapse of GBM in a human. A somatic mutation in a geneor its encoded mRNA or protein is determined in a test sample relativeto a normal sample of the human. The gene is selected from the groupconsisting of those listed in FIG. 10C. The human is identified aslikely to have glioblastoma multiforme, minimal residual disease, ormolecular relapse of GBM when the somatic mutation is determined.

Yet another aspect of the invention is a method of characterizing aglioblastoma multiforme in a human. A CAN-gene mutational signature fora glioblastoma multiforme is determined by determining in a test samplerelative to a normal sample of the human, a somatic mutation in at leastone gene or its encoded cDNA or protein. The gene is selected from thegroup consisting of those listed in FIG. 10C. The glioblastomamultiforme is assigned to a first group of glioblastoma multiformetumors that have the CAN-gene mutational signature.

Another method provided by the invention is for characterizing aglioblastoma multiforme tumor in a human. A mutated pathway selectedfrom the group consisting of TP53, RB1, and PI3K/PTEN is identified in aglioblastoma multiforme tumor by determining at least one somaticmutation in a test sample relative to a normal sample of the human. Theat least one somatic mutation is in one or more genes selected from thegroup consisting of TP53, MDM2, MDM4, RB1, CDK4, CDKN2A, PTEN, PIK3CA,PIK3R1, and IRS1. The glioblastoma multiforme is assigned to a firstgroup of glioblastoma multiforme tumors that have a mutation in one ofsaid pathways. The first group is heterogeneous with respect to thegenes in the pathway that have a somatic mutation and homogeneous withrespect to the pathway that has a somatic mutation.

Also provided is a method to detect or diagnose glioblastoma multiforme,or minimal residual disease of GBM or molecular relapse of GBM in ahuman. Expression is determined in a clinical sample of one or moregenes listed in FIG. 10 (brain overexpressed genes from SAGE). Theexpression of the one or more genes in the clinical sample is comparedto expression of the one or more genes in a corresponding sample of acontrol human or control group of humans. A clinical sample withelevated expression relative to a control is identified as likely tohave glioblastoma multiforme, or minimal residual disease of GBM ormolecular relapse of GBM in a human.

Another aspect of the invention is a method to monitor glioblastomamultiforme burden. Expression in a clinical sample is determined of oneor more genes listed in FIG. 10 (brain overexpressed genes from SAGE).The step of determining is repeated one or more times. An increase,decrease or stable level of expression over time is identified.

Yet another aspect of the invention is a method to monitor glioblastomamultiforme burden. A somatic mutation is determined in a clinical sampleof one or more genes listed in FIG. 10C. The step of determining isrepeated one or more times. An increase, decrease or stable level ofsaid somatic mutation over time is identified.

Still another aspect of the invention relates to a method to detect ordiagnose gliobastoma multiforme. Expression in a clinical sample of oneor more genes listed in FIG. 10 (homozygous deletions) is determined.Expression of the one or more genes in the clinical sample is comparedto expression of the one or more genes in a corresponding sample of acontrol human or control group of humans. A clinical sample with reducedexpression relative to a control is identified as likely to havegliobastoma multiforme.

A further aspect of the invention is a method to monitor gliobastomamultiforme burden. Expression in a clinical sample of one or more geneslisted in FIG. 10 (homozygous deletions) is determined. The step ofdetermining is repeated one or more times. An increase, decrease orstable level of expression over time is identified.

These and other embodiments which will be apparent to those of skill inthe art upon reading the specification provide the art with new toolsfor analyzing, detecting, stratifying and treating GBM.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1. Sequence alterations in IDH1. Representative examples of somaticmutations at codon 132 of the IDH1 gene. The top sequence chromatogramwas obtained from analysis of DNA from normal tissue while the lowerchromatograms were obtained from the indicated GBM samples. Arrowsindicate the location of the recurrent heterozygous missense mutationsC394A (in tumor Br104X) and G395A (in tumor Br129X) resulting in theindicated amino acid changes.

FIG. 2. Structure of the active site of IDH1. The crystal structure ofthe human cytosolic NADP(+)-dependent IDH is shown in ribbon format(PDBID: 1T0L) (42). The active cleft of IDH1 consists of a NADP-bindingsite and the isocitrate-metal ion-binding site. The alpha-carboxylateoxygen and the hydroxyl group of isocitrate chelate the Ca2+ ion. NADPis colored in orange, isocitrate in purple and Ca2+ in blue. The Arg132residue, displayed in yellow, forms hydrophilic interactions, shown inred, with the alpha-carboxylate of isocitrate.

FIG. 3. Overall survival among patients <45 years old according to IDH1mutation status. The hazard ratio for death among patients with mutatedIDH1, as compared to those with wildtype IDH1, was 0.19 (95 percentconfidence interval, 0.08 to 0.49; P<0.001). The median survival was 3.8years for patients with mutated IDH1, as compared to 1.5 years forpatients with wildtype IDH1.

FIG. 4A-4B. IDH1 and IDH2 mutations in human gliomas. FIG. 4A. Schematicdiagram of mutations at codon R132 in IDH1 (bottom) and R172 in IDH2(top) identified in human gliomas. Codons 130 to 134 of IDH1 and 170 to174 of IDH2 are shown. The number of patients with each mutation (n) islisted at the right of the figure. FIG. 4B. Number and frequency of IDH1and IDH2 mutations in human gliomas and other tumor types. The non-CNScancers included 35 lung cancers, 57 gastric cancers, 27 ovariancancers, 96 breast cancers, 114 colorectal cancers, 95 pancreaticcancers, seven prostate cancers, and peripheral blood specimens from 4chronic myelogenous leukemias, 7 chronic lymphocytic leukemias, sevenacute lymphoblastic leukemias, and 45 acute myelogenous leukemias.

FIG. 5A-5B. Survival for patients with malignant gliomas according toIDH1 and IDH2 mutation status. For patients with anaplastic astrocytomas(FIG. 5A), the median survival was 65 months for patients with mutatedIDH1 or IDH2, as compared to 19 months for patients with wildtype IDH1and IDH2. For patients with GBM (FIG. 5B), the median survival was 39months for patients with mutated IDH1 or IDH2, as compared to 13.5months for patients with wildtype IDH1 and IDH2.

FIG. 6. Model of malignant glioma development. For each tumor typecommon genetic alterations (IDH1/IDH2 mutation, TP53 mutation, 1p 19qloss, and CDKN2A loss) are indicated. Detailed frequencies of geneticalterations are contained in Table 1 and 2 or reference¹. In general,tumors on the right acquire IDH alterations, while those on the left donot.

FIG. 7. Sequence alterations in IDH1 and IDH2. Representative examplesof somatic mutations at codon 132 of the IDH1 gene (top) and codon 172of the IDH2 gene (bottom). In each case, the top sequence chromatogramwas obtained from analysis of DNA from normal tissue while the lowerchromatograms were obtained from the indicated tumor samples. Arrowsindicate the location of the missense mutations and resulting amino acidchanges in IDH1 in tumor TB2604 (anaplastic astrocytoma), 640(anaplastic astrocytoma), and 1088 (anaplastic oligodendroglioma), andin IDH2 in tumor H883 (anaplastic astrocytoma) and H476 (anaplasticoligodendroglioma).

FIG. 8. Sequence alterations in IDH1 in progressive gliomas.Representative examples of somatic mutations at codon 132 of the IDH1are indicated in three representative cases. The top sequencechromatogram was obtained from analysis of DNA from normal tissue whilethe lower chromatograms were obtained from the indicated brain tumorsamples. Arrows indicate the location of the mutations and the resultingamino acid changes in IDH1. In all cases, the identical IDH1 mutationswere found in the lower- and higher-grade tumors from each patient.

FIG. 9A-9B. Age distribution of glioma patients with mutated andwild-type IDH. Age distribution of oligodendroglioma (O), anaplasticaoligodendroglioma (AO), diffuse astrocytoma (DA), anaplastic astrocytoma(AA), and glioblastoma multiforme (GBM) in patients with wild-type IDHgenes (FIG. 9A) or mutated IDH genes (FIG. 9B).

FIG. 10A-C. Table S3 (somatic mutations identified in GBM discoveryscreen, FIG. 10A). Table S4 (somatic mutations in prevalence screen,FIG. 10B). Table S7 (top CAN-candidate genes, FIG. 10C).

FIG. 11. Summary of genetic and clinical characteristics of braintumors.

FIG. 12. Evaluation of frequency of common genetic alterations inIDH1/IDH2 mutated and wildtype gliomas.

FIG. 13. Bioinformatics software pipeline to compute mutation scores.

A sequence listing is part of this application.

DETAILED DESCRIPTION OF THE INVENTION

In a genome-wide analysis of GBMs, we identified somatic mutations ofcodon 132 of the isocitrate dehydrogenase 1 gene (IDH1) in ˜12% of GBMsanalyzed¹⁶. These mutations were found at higher frequency in secondaryGBMs (5 of 6 patients evaluated). One interpretation of these data isthat IDH1 mutations occur in a subset of lower-grade gliomas, drivingthem to progress to GBMs. To evaluate this possibility, we have analyzeda large number of gliomas of various types. Remarkably, we found IDH1mutations in the majority of early malignant gliomas. Furthermore, manyof the gliomas without IDH1 mutations had analogous mutations in theclosely related IDH2 gene. These results suggest that IDH mutations playan early and essential role in malignant glioma development.

Somatic mutations are mutations which occur in a particular clone ofsomatic cells during the lifetime of the individual organism. Themutation is thus not inherited or passed on. The mutation will appear asa difference relative to other cells, tissues, organs. When testing fora somatic mutation in a brain tissue suspected of being cancerous, acomparison can be made to normal brain tissue that appears to benon-neoplastic, or to a non-brain sample, such as blood cells, or to asample from an unaffected individual.

The common amino acid at codon 132 of IDH1 and codon 172 of IDH2 inhealthy tissues is arginine (R). Mutant codons have been found withsubstitutions of histidine (H), serine (S), and cysteine (C), leucine(L), and glycine (G) of IDH1 codon 132 and of methionine (M), lysine(K), and glycine (G) of codon 172 of IDH2. The mutations at codon 132and codon 172 can be detected using any means known in the art,including at the DNA, mRNA, or protein levels. Antibodies whichspecifically bind to the arginine-132 form of the enzyme, thehistidine-132 form of the enzyme, the serine-132 form of the enzyme,leucine-132 form of the enzyme, glycine-132 form of the enzyme, or thecysteine-132 form of the enzyme can be used in assays for mutationdetection. Likewise antibodies which specifically bind to thearginine-172, methionine-172, lysine-172, or glycine-172 forms of IDH2can be used in assays for mutation detection. Similarly, probes whichcontain codons for these amino acid residues in the context of thecoding sequence of IDH1 or IDH2 can be used for detecting the gene ormRNA of the different forms. Primers which contain all or part of thesecodons can also be used for allele-specific amplification or extension.Primers hybridizing to regions surrounding these codons can be used toamplify the codons, followed by subsequent analysis of the amplifiedregion containing codon 132 of IDH1 or codon 172 of IDH2.

Interestingly, the codon 132 mutations of IDH1 and codon 172 mutationsof IDH2 have been found to be strongly associated with secondary GBM andwith a favorable prognosis. Drugs can be tested against groups ofglioblastoma patients that are stratified with regard to the 132^(nd)amino acid residue of IDH1 and/or the 172^(nd) amino acid residue ofIDH2. The groups may comprise wild-type (arginine) and variants(combined) or variants (each separately). Drug sensitivity can bedetermined for each group to identify drugs which will or will not beefficacious relative to a particular mutation or wild-type (arginine).Both sensitivity and resistance information are useful to guidetreatment decisions.

Once a codon 132 or 172 mutation is identified in a tumor, inhibitors ofIDH1 or IDH2 may be used therapeutically. Such inhibitors may bespecific for a mutation in the tumor or may simply be an inhibitor ofIDH1 or IDH2. Small molecule inhibitors as well as antibodies andantibody-derivatives can be used. Such antibodies include monoclonal andpolyclonal antibodies, ScFv antibodies, and other constructs whichcomprise one or more antibody Fv moieties. Antibodies can be humanized,human, or chimeric, for example. Antibodies may be armed or unarmed.Armed antibodies may be conjugated to toxins or radioactive moieties,for example. Unarmed antibodies may function to bind to tumor cells andparticipate in host immunological processes, such as antibody-dependentcell-medicated cytotoxicity. Antibodies may preferentially bind tomutant versus wild-type IDH1 or IDH2, specifically bind to mutant versuswild-type IDH1 or IDH2, or bind equally to both mutant and wild-typeIDH1 or IDH2. Preferably the antibodies will bind to an epitope in theactive site which may include codon 132 or codon 172. Epitopes may becontinuous or discontinuous along the primary sequence of the protein.Inhibitors may include alpha-methyl isocitrate, aluminum ions, oroxalomalate. Other inhibitors may be used and optionally identifiedusing enzyme assays known in the art, including spectrophotometricassays (Kornberg, A., 1955) and bioluminescent assays (Raunio, R. etal., 1985). Inhibitors may be alternatively identified by binding tests,for example by in vitro or in vivo binding assays. Peptides and proteinswhich bind to IDH1 or IDH2 may also be used as inhibitors.

Inhibitory RNA molecules may be used to inhibit expression. These maybe, for example, siRNA, microRNA or antisense oligonucleotides orconstructs. These can be used to inhibit the expression of IDH1 or IDH2as appropriate in a human.

Potential therapeutic efficacy can be tested for an antibody,polynucleotide, protein, small molecule, or antibody by contacting withcells, tissues, whole animals, or proteins. Indications of efficacyinclude modulation of enzyme activity, inhibition of cancer cell growth,prolongation of life expectancy, inhibition of cancer cellproliferation, stimulation of cancer cell apoptosis, and inhibition orretardation of tumor growth. Any assays known in the art can be used,without limitation. Combinations of candidates and combinations ofcandidates with known agents can be assessed as well. Known agents mayinclude, for example, chemotherapeutic anti-cancer agents, biologicalanti-cancer agents, such as antibodies and hormones, radiation.

In order to raise or increase an immune response to a glioblastoma in aperson or mammal with a tumor, in a person with a likelihood ofdeveloping a tumor, or in an apparently healthy individual, apolypeptide can be administered to the person or mammal. The polypeptidewill typically comprise at least 6, at least 8, at least 10, at least12, or at least 14 contiguous amino acid residues of human IDH1 proteinincluding residue 132 or IDH2 including residue 172. Typically but notalways, the polypeptide will contain a residue other than arginine atresidue 132 of IDH1 or residue 172 or IDH2. In the situation where theperson or mammal already has a tumor, the amino acid at residue 132 canbe matched to the residue in the tumor. The polypeptide may comprise thewhole of IDH1, but can comprise less than 200, less than 150, less than100, less than 50, less than 30 amino acid residues. Although applicantsdo not wish to be bound by any mechanism of action, the polypeptideimmunization may act though an antibody and/or T cell response.Polypeptides can be administered with immune adjuvants or conjugated tomoieties which stimulate an immune response. These are well known in theart, and can be used as appropriate.

Antibodies which specifically bind to an epitope on IDH1 or IDH2 do sowith a higher avidity or a higher association rate than they bind toother proteins. Preferably the higher avidity or rate of association isat least about 2-fold, 5-fold, 7-fold, or 10-fold relative to otherproteins that do not contain the epitope.

An isolated polynucleotide can be used to encode and deliver thepolypeptide for immunization. The polynucleotide can be used tomanufacture the polypeptide in a host cell in culture, or may be used ina gene therapy context to raise an immune response in vivo uponexpression in the vaccine recipient. Polynucleotides can also be used asprimers or probes, which may or may not be labeled with a detectablelabel. Primers can be used for primer extension, for example, using aprimer that is complementary to nucleotides adjacent to but notincluding either nt 394 or nt 395 of IDH1 or nucleotide 515 of IDH2.Products can be detected and distinguished using labeled nucleotides asreagents. Different labels may be used on different nucleotides so thatthe identity of the analyte can be readily determined. Typically thepolynucleotide for use as a primer or probe will comprise at least 10,at least 12, at least 14, at least 16, at least 18, at least 20contiguous nucleotides of IDH1 or IDH2 coding sequence. Typically thepolynucleotide will comprise less than 600, less than 500, less than400, less than 300, less than 200, less than 100 nucleotides of IDH1 orIDH2 coding sequence.

Our data identified IDH1 as a major target of genetic alteration inpatients with GBM. All mutations in this gene resulted in amino acidsubstitutions at position 132, an evolutionarily conserved residuelocated within the isocitrate binding site (42). In addition, the onlypreviously-reported mutation of IDH1 was another missense mutationaffecting this same residue in a colorectal cancer patient (10). Thefunctional effect of these IDH1 mutations is unclear. The recurrentnature of the mutations is reminiscent of activating alterations inother oncogenes such as BRAF, KRAS, and PIK3CA. The prediction that thismutation would be activating is strengthened by the lack of observedinactivating changes (i.e. frameshift or stop mutations, splice sitealterations), the lack of alterations in other key residues of theactive site, and by the fact that all mutations observed to date wereheterozygous (without any evidence of loss of the second allele throughLOH). Interestingly, enzymatic studies have shown that substitution ofarginine at residue 132 with glutamate results in a catalyticallyinactive enzyme suggesting that this residue plays a critical role inIDH1 activity (46). However, the nature of the substitutions observed inGBMs is qualitatively different, with arginine changed to histidine orserine. Histidine forms hydrogen bonding interactions with carboxylateas part of the catalytic activity of many enzymes (47), and could servean analogous function to the known interaction of Arg132 and theα-carboxylate of isocitrate. It is conceivable that R132H alterationsmay lead to higher overall catalytic activity. Increased activity ofIDH1 would be expected to result in higher levels of NADPH, providingadditional cellular defenses against reactive oxygen species, preventingapoptosis and increasing cellular survival and tumor growth. Furtherbiochemical and molecular analyses will be needed to determine theeffect of alterations of IDH1 on enzymatic activity and cellularphenotypes.

Regardless of the specific molecular consequences of IDH1 and IDH2alterations, it is clear that detection of mutations in IDH1 and IDH2will be clinically useful. Although significant effort has focused onthe identification of characteristic genetic lesions in primary andsecondary GBMs, the altered genes identified to date are far fromperfect for this purpose. For example, in comparing primary versussecondary GBMs, TP53 is mutated in ˜30% vs. 65%, respectively, EFGRamplification is present in ˜35% vs. 5-10%, and PTEN mutation is presentin ˜25% vs. ˜5% (5). Our study revealed IDH1 mutation to be a novel andsignificantly more specific marker for secondary GBM, with 5 of the 6(83%) secondary GBM samples analyzed having a mutation in this gene,while only 7 of 99 (7%) primary GBM patients had such alterations(P<0.001, binomial test). The sole secondary GBM patient sample that didnot have an IDH1 mutation was both genetically and clinically unusual,harboring mutations of PTEN but not TP53, and occurring in an olderpatient (age 56 years) with a prior diagnosis of ganglioglioma (which israrely known to undergo malignant transformation) (48). It is possiblethat this patient had two distinct CNS tumors which were completelyunrelated, and that the GBM in this case was actually a primary tumor.

One intriguing hypothesis is that IDH1 alterations identify abiologically-specific subgroup of GBM patients, including both patientswho would be classified as having secondary GBMs as well as asubpopulation of primary GBM patients with a similar tumor biology andmore protracted clinical course (Table 4). Interestingly, patients withIDH1 mutations had a very high frequency of TP53 mutation and a very lowfrequency of mutations in other commonly-altered GBM genes. For example,such patients had TP53 mutation without any detected mutation of EGFR,PTEN, RB1, or NF1 in 83% of cases (10 of 12 patients); in contrast, only12% of patients with wildtype IDH1 (11 of 93) had the same mutationpattern (FIG. 12)(P<0.001, binomial test). In addition to this relativegenetic uniformity, the patients with mutated IDH1 had distinct clinicalcharacteristics, including younger age and a significantly improvedclinical prognosis (Table 4) even after adjustment for age and TP53mutation status (both of which are associated with improved survival).Perhaps most surprisingly, they all shared mutation of a single aminoacid residue of IDH1, a protein that previously had no genetic link toGBMs or other cancers. This unforeseen result clearly validates theutility of genome-wide screening for genetic alterations in the study ofhuman cancers.

Mutations that have been found in GBM tumors are shown in FIG. 10, TableS7. These mutations can be detected in test samples, such as suspectedtumor tissue samples, blood, CSF, urine, saliva, lymph etc. A somaticmutation is typically determined by comparing a sequence in the testsample to a sequence in a normal control sample, such as from healthybrain tissue. One or more mutations can be used for this purpose. If thepatient has undergone surgery, detection of the mutation in tumor marginor remaining tissue can be used to detect minimal residual disease ormolecular relapse. If GBM has been previously undiagnosed, the mutationmay serve to help diagnose, for example in conjunction with otherphysical findings or laboratory results, including but not limited tobiochemical markers and radiological findings.

CAN-gene signatures can be determined in order to characterize a GBM. Asignature is a set of one or more somatic mutations in a CAN gene. TheCAN genes for GBM are listed in FIG. 10C, Table S7. Once such asignature has been determined, a GBM can be assigned to a group of GBMssharing the signature. The group can be used to assign a prognosis, toassign to a clinical trial group, to assign to a treatment regimen,and/or to assign for further characterization and studies. In a clinicaltrial group, drugs can be assessed for the ability to differentiallyaffect GBMs with and without the signature. Once a differential effectis determined, the signature can be used to assign patients to drugregimens, or to avoid unnecessarily treating patients in whom the drugwill not have a beneficial effect. The drug in a clinical trial can beone which is previously known for another purpose, previously known fortreating GBM, or previously unknown as a therapeutic. A CAN-genesignature may comprise at least 1, at least 2, at least 3, at least 4,at least 5, at least 6, at least 7, at least 8, at least 9. at least 10genes. The number of genes or mutations in a particular signature mayvary depending on the identity of the CAN genes in the signature.Standard statistical analyses can be used to achieve desired sensitivityand specificity of a CAN gene signature.

Analysis of the mutated genes in the analyzed GBM tumors has revealedinteresting involvement of pathways. Certain pathways frequently carrymutations in GBMs. A single gene mutation appears to exclude thepresence of a mutation in another gene in that pathway in a particulartumor. Frequently mutated pathways in GBMs are the TP53, RB1, PI3K/PTENpathways. Pathways can be defined using any of the standard referencedatabases, such as MetaCore Gene Ontology (GO) database, MetaCorecanonical gene pathway maps (MA) database, MetaCore GeneGo (GG)database, Panther, TRMP, KEGG, and SPAD databases. Groups can be formedbased on the presence or absence of a mutation in a certain pathway.Such groups will be heterogeneous with respect to mutated gene buthomogeneous with respect to mutated pathway. As with CAN genesignatures, these groups can be used to characterize a GBM. Once amutation in a pathway has been determined, a GBM can be assigned to agroup of GBMs sharing the mutated pathway. The group can be used toassign a prognosis, to assign to a clinical trial group, to assign to atreatment regimen, and/or to assign for further characterization andstudies. In a clinical trial group, drugs can be assessed for theability to differentially affect GBMs with and without the mutatedpathway. Once a differential effect is determined, the pathway can beused to assign patients to drug regimens, or to avoid unnecessarilytreating patients in whom the drug will not have a beneficial effect.The drug in a clinical trial can be one which is previously known foranother purpose, previously known for treating GBM, or previouslyunknown as a therapeutic. Among the genes in the pathways which may befound mutant are: TP53, MDM2, MDM4, RB1, CDK4, CDKN2A, PTEN, PIK3CA,PIK3RI, and IRS 1. This list is not necessarily exhaustive.

Expression levels can be determined and overexpression may be indicativeof a new GBM tumor, molecular relapse, or minimal residual disease ofGBM. These overexpressed genes can be detected in test samples, such assuspected tumor tissue samples, blood, CSF, urine, saliva, lymph etc.Elevated expression is typically determined by comparing expression of agene in the test sample to expression of a gene in a normal controlsample, such as from healthy brain tissue. Elevated expression of one ormore genes can be used for this purpose. If the patient has undergonesurgery, detection of the elevated expression in tumor margin orremaining tissue can be used to detect minimal residual disease ormolecular relapse. If GBM has been previously undiagnosed, the elevatedexpression may serve to help diagnose, for example in conjunction withother physical findings or laboratory results, including but not limitedto biochemical markers and radiological findings. For these purposes,any means known in the art for quantitating expression can be used,including SAGE or microarrays for detecting elevated mRNA, andantibodies used in various assay formats for detecting elevated proteinexpression.

Tumor burden can be monitored using the mutations listed in FIG. 10C,Table S7. This may be used in a watchful waiting mode, or during therapyto monitor efficacy, for example. Using a somatic mutation as a markerand assaying for level of detectable DNA, mRNA, or protein over time,can indicate tumor burden. The level of the mutation in a sample mayincrease, decrease or remain stable over the time of analysis.Therapeutic treatments and timing may be guided by such monitoring.

Analysis of the GBMs revealed certain genes which are homozygouslydeleted. These are listed in FIG. 10. Determining loss of expression ofone or more of these genes can be used as a marker of GBM. This may bedone in a sample of blood or lymph node or in a brain tissue sample.Expression of one or more of these genes may be tested. Techniques suchas ELISA or IHC may be used to detect diminution or loss of proteinexpression in a sample. Similarly homozygously deleted genes may be usedto monitor tumor burden over time. Expression can be repeatedlymonitored so that in increase, decrease, or stable level of expressioncan be ascertained.

The data resulting from this integrated analysis of mutations and copynumber alterations have provided a novel view of the genetic landscapeof glioblastomas. The combination of different types of genetic data,including point mutations, amplifications, and deletions allows foridentification of individual CAN-genes as well as groups of genes thatmay be preferentially affected in complex cellular pathways andprocesses in GBMs. Identification of virtually all genes previouslyshown to be affected in GBMs by mutation, amplification, or deletionvalidates the comprehensive genomic approach we have employed.

It should be noted, however, that our approach, like all genome-widestudies, has limitations. First we did not assess chromosomaltranslocations, which is one type of genetic alteration that could playan important role in tumorigenesis. However, observations of recurrentchromosomal translocations have only rarely been reported incyotogenetic studies of GBM. We also did not assess epigeneticalterations, though our large scale expression studies should haveidentified any genes that were differentially expressed through thismechanism. Additionally, for copy number changes we focused on regionsthat were truly amplified or homozygously deleted as these havehistorically been most useful in identifying cancer genes. The SNP arraydata we have generated for these samples, however, contains informationthat can be analyzed to determine loss of heterozygosity (LOH) or smallcopy number gains due to duplications rather than true amplificationevents. Analysis of such data for known cancer genes, such as CDKN2A orNF1, identified additional tumors that had LOH in these regions, butgiven the substantial fraction of the genome that undergoes LOH in GBMs,such observations are in general not likely to be helpful in pinpointingnew candidate cancer genes. Finally, the primary tumors used in ouranalysis contained small amounts of contaminating normal tissue, as isthe rule for this sample type, which limited our ability to detecthomozygous deletions and to a lesser extent, somatic mutations, in thosespecific tumors. This was true even though we carefully selected thesetumors to contain a minimal stromal component by histological andmolecular biologic criteria. This observation serves as an importantreminder of the value of early passage xenografts and cell lines forsuch large scale genomic studies.

Despite these limitations, our studies provide a number of importantgenetic and clinical insights into GBMs. The first of these is that thepathways known to be altered in GBMs affect a larger fraction of genemembers and patients than previously anticipated. A majority of thetumors analyzed had alterations in members of each of the TP53, RB1, andPI3K pathways. The fact that all but one of the cancers with mutationsin members of a pathway did not have alterations in other members of thesame pathway is significant and suggests that such alterations arefunctionally equivalent in tumorigenesis. These observations also pointto distinct opportunities for potential therapeutic intervention inthese pathways in GBMs. The second observation is that a variety of newgenes and pathways not previously implicated in GBMs were identified.Among the new pathways detected, a number of these appear to be involvedin brain specific ion transport and signaling processes and representinteresting and potentially useful aspects of GBM biology.

These data immediately raise questions with important implications forthe treatment and counseling of patients with GBMs as well as those withlower-grade gliomas. For example, are mutations in IDH also present in asubset of patients diagnosed with lower-grade gliomas (WHO gradesI-III)? If IDH1 mutations are indeed found to be a relatively earlygenetic event in glioma progression, are these patients at increasedrisk of progression to GBM? Given the significant clinical difficulty ofdeciding which low grade glioma patients will receive adjuvant radiationtherapy or chemotherapy (and how aggressive treatment should be), theknowledge that a patient is at increased risk for malignant progressionwould significantly alter the risk-benefit analysis of such treatmentdecisions. For pediatric patients, in whom radiation therapy can haveparticularly devastating effects on neurocognitive development andfunction, these decisions are particularly difficult and any additionalrisk-classification would be especially useful. IDH mutations may alsoprovide one biological explanation for the occasional long-term GBMsurvivor, and could help to identify patients that would receiveparticular benefit from specific currently-available therapies. Theutility of IDH as a clinical marker is likely to be enhanced by the factthat only a single codon of the gene needs to be examined to determinemutation status. Finally, it is conceivable that new treatments may bedesigned to take advantage of these IDH alterations, either asmonotherapy or in combination with other agents. Along these lines,inhibition of mitochondrial IDH2 has recently been shown to result inincreased sensitivity of tumor cells to a variety of chemotherapeuticagents (49). In summary, this finding of IDH mutations in a subset ofGBM patients and in at least one other cancer type opens a new avenue ofresearch that could illuminate a previously unappreciated aspect ofhuman tumorigenesis.

The above disclosure generally describes the present invention. Allreferences disclosed herein are expressly incorporated by reference. Amore complete understanding can be obtained by reference to thefollowing specific examples which are provided herein for purposes ofillustration only, and are not intended to limit the scope of theinvention.

Example 1

Materials and Methods

DNA was extracted from primary tumor and xenograft samples andpatient-matched normal blood lymphocytes obtained from the Tissue Bankat the Preston Robert Tisch Brain Tumor Center at Duke and collaboratingcenters, as previously described¹⁷. All brain tumors analyzed weresubjected to consensus review by two neuropathologists. The panel ofbrain tumors consisted of 21 pilocytic astrocytomas and 2 subependymalgiant cell gliomas (WHO Grade I); 31 diffuse astrocytomas, 51oligodendrogliomas, three oligoastrocytomas, 30 ependymomas, and sevenpleomorphic xanthoastrocytomas (WHO Grade II); 43 anaplasticastrocytomas, 36 anaplastic oligodendrogliomas, and seven anaplasticoligoastrocytomas (WHO Grade III); 178 GBMs and 55 medulloblastomas (WHOGrade IV). The GBM samples included 165 primary and 13 secondary cases.Fifteen of the GBMs were from patients <20 years old). Secondary GBMswere defined as those that were resected >1 year after a prior diagnosisof a lower grade glioma (WHO Grades Sixty-six of the 178 GBMs, but noneof the lower grade tumors, had been analyzed in our prior genome-widemutation analysis of GBMs¹⁶. In addition to the brain tumors, 494non-CNS cancers were examined: 35 lung cancers, 57 gastric cancers, 27ovarian cancers, 96 breast cancers, 114 colorectal cancers, 95pancreatic cancers, seven prostate cancers, 4 chronic myelogenousleukemias, 7 chronic lymphocytic leukemias, 7 acute lymphoblasticleukemias, and 45 acute myelogenous leukemias. All samples were obtainedin accordance with the Health Insurance Portability and AccountabilityAct. Acquisition of tissue specimens was approved by the Duke UniversityHealth System Institutional Review Board and the corresponding IRBs atcollaborating institutions.

Exon 4 of the IDH1 gene was PCR-amplified and sequenced in the matchedtumor and normal DNAs for each patient as previously described¹⁶. Inselected patients without an R132 IDH1 mutation (those with Grade II orIII lesions or secondary GBM), the remaining seven exons of IDH1 and all11 exons of IDH2 were sequenced and analyzed for mutations. All codingexons of TP53 and PTEN were also sequenced in the panel ofoligodendrogliomas, anaplastic oligodendrogliomas, anaplasticastrocytomas, and GBMs. EGFR amplification and CDKN2A/CDKN2B deletionwere analyzed by quantitative real-time PCR in the same tumors¹⁸.Oligodendroglioma and anaplastic oligodendroglioma samples wereevaluated for loss of heterozygosity (LOH) at 1p and 19q as previouslydescribed^(15, 19).

Clinical information included date of birth, date the study sample wasobtained, date of pathologic diagnosis, date and pathology of anypreceding diagnosis of a lower grade glioma, administration of radiationtherapy and/or chemotherapy prior to the date that the study sample wasobtained, date of last patient contact, and patient status at lastcontact. Clinical information for survival analysis was available forall 482 primary brain tumor patients. Kaplan-Meier survival curves wereplotted and the survival distributions were compared by the Mantel Coxlog-rank test and the Wilcoxon test. Overall survival was calculated byusing date of GBM diagnosis and date of death or last patient contact.The correlations between the occurrence of IDH1/IDH2 mutations and othergenetic alterations were examined using Fisher's exact test.

Example 2

High Frequency Alterations of IDH1 in Young GBM Patients

The top CAN-gene list included a number of individual genes which hadnot previously been linked to GBMs. The most frequently mutated of thesegenes, IDH1, encodes isocitrate dehydrogenase 1, which catalyzes theoxidative carboxylation of isocitrate to α-ketoglutarate, resulting inthe production of NADPH. Five isocitrate dehydrogenase genes are encodedin the human genome, with the products of three (IDH3 alpha, IDH3 beta,IDH3 gamma) forming a heterotetramer (a2f3y in the mitochondria andutilizing NAD(+) as an electron acceptor to catalyze the rate-limitingstep of the tricarboxylic acid cycle. The fourth isocitratedehydrogenase (IDH2) is also localized to the mitochondria, but likeIDH1, uses NADP(+) as an electron acceptor. The IDH1 product, unlike therest of the IDH proteins, is contained within the cytoplasm andperoxisomes (41). The protein forms an asymmetric homodimer (42), and isthought to function to regenerate NADPH and α-ketoglutarate forintraperoxisomal and cytoplasmic biosynthetic processes. The productionof cytoplasmic NADPH by IDH1 appears to play a significant role incellular control of oxidative damage (43) (44). None of the other IDHgenes, other genes involved in the tricarboxylic acid cycle, or otherperoxisomal proteins were found to be genetically altered in ouranalysis.

IDH1 was found to be somatically mutated in five GBM tumors in theDiscovery Screen. Surprisingly, all five had the same heterozygous pointmutation, a change of a guanine to an adenine at position 395 of theIDH1 transcript (G395A), leading to a replacement of an arginine with ahistidine at amino acid residue 132 of the protein (R132H). In our priorstudy of colorectal cancers, this same codon had been found to bemutated in a single case through alteration of the adjacent nucleotide,resulting in a R132C amino acid change (10). Five additional GBMsevaluated in our Prevalence Screen were found to have heterozygous R132Hmutations, and an additional two tumors had a third distinct mutationaffecting the same amino acid residue, R132S (FIG. 1; Table 4). The R132residue is conserved in all known species and is localized to thesubstrate binding site, forming hydrophilic interaction with thealpha-carboxylate of isocitrate (FIG. 2) (42, 45).

Several important observations were made about IDH1 mutations and theirpotential clinical significance. First, mutations in IDH1 preferentiallyoccurred in younger GBM patients, with a mean age of 33 years forIDH1-mutated patients, as opposed to 53 years for patients with wildtypeIDH1 (P<0.001, t-test, Table 4. In patients under 35 years of age,nearly 50% (9 of 19) had mutations in IDH1. Second, mutations in IDH1were found in nearly all of the patients with secondary GBMs (mutationsin 5 of 6 secondary GBM patients, as compared to 7 of 99 patients withprimary GBMs, P<0.001, binomial test), including all five secondary GBMpatients under 35 years of age. Third, patients with IDH1 mutations hada significantly improved prognosis, with a median overall survival of3.8 years as compared to 1.1 years for patients with wildtype IDH1(P<0.001, log-rank test). Although younger age and mutated TP53 areknown to be positive prognostic factors for GBM patients, thisassociation between IDH1 mutation and improved survival was noted evenin patients <45 years old (FIG. 3, P<0.001, log-rank test), as well asin the subgroup of young patients with TP53 mutations (P<0.02, log-ranktest).

Example 3

Glioblastoma Multiforme (GBM) DNA Samples

Tumor DNA was obtained from GBM xenografts and primary tumors, withmatched normal DNA for each case obtained from peripheral blood samples,as previously described (1). All samples were given the histologicdiagnosis of glioblastoma multiforme (GBM; World Health OrganizationGrade IV), except for two Discovery Screen samples who were recorded as“high grade glioma, not otherwise specified”. Samples were classified asrecurrent for patients in whom a GBM had been diagnosed at least 3months prior to the surgery when the study GBM sample was obtained.There were 3 recurrent GBMs in the Discovery Screen, and 15 in thePrevalence Screen. Samples were classified as secondary for patients inwhom a lower grade glioma (WHO grade I-III) had been histologicallyconfirmed at least 1 year prior to the surgery when the study GBM samplewas obtained. One Discovery Screen sample and 5 Prevalence Screensamples were classified as secondary.

Pertinent clinical information, including date of birth, date study GBMsample obtained, date of original GBM diagnosis (if different than thedate that the GBM sample was obtained, as in the case of recurrentGBMs), date and pathology of preceding diagnosis of lower grade glioma(in cases of secondary GBMs), the administration of radiation therapyand/or chemotherapy prior to the date that the GBM sample was obtained,date of last patient contact, and patient status at last contact. Allsamples were obtained in accordance with the Health InsurancePortability and Accountability Act (HIPAA). All samples were obtained inaccordance with the Health Insurance Portability and Accountability Act(HIPAA). As previously described, tumor-normal pair matching wasconfirmed by typing nine STR loci using the PowerPlex 2.1 System(Promega, Madison, Wis.) and sample identities checked throughout theDiscovery and Prevalence screens by sequencing exon 3 of the HLA-A gene.PCR and sequencing was carried out as described in (1).

Example 4

Statistical Analysis of Clinical Data

Paired normal and malignant tissue from 105 GBM patients were used forgenetic analysis. Complete clinical information (i.e. all pertinentclinical information such as date of initial GBM diagnosis, date ofdeath or last contact) was available for 91 of the 105 patients. Ofthese 91 patients, five (all IDH1-wildtype) died within the first monthafter surgery and were excluded from analysis (Br308T, Br246T, Br23X,Br301T, Br139X), as was a single patient (Br119X) with a presumedsurgical cure (also IDH1-wildtype) who was alive at last contact ˜10years after diagnosis. Kaplan Meier survival curves were compared usingthe Mantel Cox log-rank test. Hazard ratios were computed using theMantel-Haenszel method. The following definitions were used in the GBMpatient grouping and survival analysis computations: 1) Patient agereferred to the age at which the patient GBM sample was obtained. 2)Recurrent GBM designates a GBM which was resected >3 months after aprior diagnosis of GBM. 3) Secondary GBM designates a GBM which wasresected >1 year after a prior diagnosis of a lower grade glioma (WHO 4)Overall survival was calculated using date of GBM diagnosis and date ofdeath or last patient contact. All confidence intervals were calculatedat the 95% level.

Example 5

IDH1 and IDH2 Mutations

Sequence analysis of IDH1 in 976 tumor samples revealed a total of 167somatic mutations at residue R132, including R132H (148 tumors), R132C(8 tumors), R132S (2 tumors), R132L (8 tumors) and R132G (1 tumor) (FIG.4A, FIG. 7). Tumors with somatic R132 mutations included 25 of 31 (81%)diffuse astrocytomas (WHO Grade II), 41 of 51 (80%) oligodendrogliomas(WHO Grade II), 3 of 3 (100%) oligoastrocytomas (WHO Grade II), one of 7(14%) pleomorphic xanthoastrocytomas (WHO Grade II), 41 of 61 (67%)anaplastic astrocytomas (WHO Grade III), 31 of 36 (86%) anaplasticoligodendrogliomas (WHO Grade III), 7 of 7 (100%) anaplasticoligoastrocytomas (WHO grade III), 11 of 13 (85%) secondary GBMs, and 7of 165 (4%) primary GBMs (FIG. 1B, FIG. 11). In contrast, no R132mutations were observed in 21 pilocytic astrocytomas (WHO Grade I), twosubependymal giant cell astrocytomas (WHO Grade I), 30 ependymomas (WHOGrade II), 55 medulloblastomas, or in any of the 494 non-CNS tumorsamples. Sequence analysis of the remaining IDH1 exons revealed no othersomatic mutations of IDH1 in the R132-negative tumors.

If IDH1 were critical to the development or progression ofoligodendrogliomas and astrocytomas, we reasoned that alterations inother genes with similar functions to IDH1 might be found in those inthose tumors without IDH1 mutations. We therefore analyzed the IDH2gene, which encodes the only human protein homologous to IDH1 thatutilizes NADP+ as an electron acceptor. Sequence evaluation of all IDH2exons in these samples, revealed eight somatic mutations, all at residueR172: R172M in three tumors, R172K in three tumors, and R172G in twotumors (FIG. 1A, FIG. 7). The R172 residue in IDH2 is the exact analogueof the R132 residue of IDH1, which is located in the active site of theenzyme and forms hydrogen bonds with the isocitrate substrate.

To further evaluate the timing of IDH alterations in glioma progression,we assessed IDH1 mutations in seven patients with progressive gliomas inwhich both low- and high-grade tumor samples were available. Sequenceanalysis identified IDH1 mutations in both the low and high-grade tumorsin all seven cases (FIG. 8, Table 4). These results unambiguouslydemonstrate that IDH1 alterations occur in low-grade tumors and thatsubsequent cancers in such patients are directly derived from theseearly lesions.

We also examined the oligodendrogliomas, anaplastic oligodendrogliomas,anaplastic astrocytomas, and a subset of GBMs for mutations of TP53 andPTEN, amplification of EGFR, deletion of CDKN2A/CDKN2B, and LOH of1p/19q (FIG. 12). TP53 mutations were much more common in anaplasticastrocytomas (63%) and secondary GBMs (60%) than in oligodendrogliomas(16%) or anaplastic oligodendrogliomas (10%) (p<0.001, Fisher's exacttest). Conversely, deletions of 1p and 19q were found more often inoligodendrocytic than astrocytic tumors, as expected 15.

Comparison of these alterations with those in IDH1 and IDH2 revealedseveral striking correlations. Nearly all of the anaplastic astrocytomasand GBMs with mutated IDH1/IDH2 also had mutation of TP53 (82%), butonly 5% had any alteration of PTEN, EGFR, or CDKN2A/CDKN2B (FIG. 12).Conversely, anaplastic astrocytomas and GBMs with wild-type IDH1 had fewTP53 mutations (21%) and more frequent alterations of PTEN, EGFR, orCDKN2A/CDKN2B (40%) (p<0.001, Fisher's exact test). Loss of 1p/19q wasobserved in 85% ( 45/53) of the oligodendrocytic tumors with mutatedIDH1 or IDH2 but in none (0/9) of the patients with wild-type IDH genes(p<0.001, Fisher's exact test).

Patients with anaplastic astrocytomas and GBMs with IDH1 or IDH2mutations were significantly younger than those with wild-type IDH1 andIDH2 genes (median age of 34 years vs. 58 years, p<0.001, Student'st-test). Interestingly, despite the lower median age of patients withIDH1 or IDH2 mutations, no mutations were identified in GBM frompatients who were less than 20 years old (0 of 18 patients, FIG. 9). Inpatients with oligodendrogliomas and anaplastic oligodendrogliomas, themedian age of the patients with IDH1 or IDH2 mutation was 39 years, withIDH1 mutations identified in two teenagers (14 and 16 yrs), but not inyounger patients (0 of 4).

Our prior observation of improved prognosis for GBM patients withmutated IDH1 16 was confirmed in this larger data set and extended toinclude patients with mutations in IDH2. Patients with IDH1 or IDH2mutations had a median overall survival of 39 months, significantlylonger than the 13.5 month survival in patients with wild-type IDH1(FIG. 5, p<0.001, log-rank test). Mutations of IDH genes were alsoassociated with improved prognosis in patients with anaplasticastrocytomas (WHO Grade III), with median overall survival of 65 monthsfor patients with mutations and 19 months for those without (p<0.001,log-rank test). Differential survival analyses could not be performed inpatients with diffuse astrocytomas, oligodendrogliomas, or anaplasticoligodendrogliomas because there were so few tumors of these typeswithout IDH gene mutations.

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The disclosure of each reference cited is expressly incorporated herein.The references in the following list are cited in the text withsuperscript reference numerals.

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Example 6

Sequencing Strategy

We extended our previously-developed sequencing strategy foridentification of somatic mutations to include 23,219 transcripts from20,583 genes. These included 2783 additional genes from the Ensembldatabases that were not present in the CCDS or RefSeq databases analyzedin previous studies (10, 11). In addition, we redesigned PCR primers forregions of the genome that (i) were difficult to PCR amplify and hadbeen sub-optimally analyzed in prior studies; or (ii) were found toshare significant identity with other human or mouse sequences. Thecombination of these new, redesigned, and existing primers sequencesresulted in a total of 208,311 primer pairs (table 51; available on-lineat Science 26 Sep. 2008: Vol. 321. no. 5897, pp. 1807-1812) that weresuccessfully used for sequence analysis of the coding exons of thesegenes.

Twenty-two GBM samples were selected for PCR sequence analysis,consisting of 7 samples extracted directly from patient tumors and 15tumor samples passaged in nude mice as xenografts. One tumor (Br27P) wasa secondary GBM obtained from a patient who had previously been treatedwith both radiation therapy and chemotherapy, including temozolomide.All other tumors were categorized as primary GBMs and had not receivedtumor-directed treatment prior to the acquisition of the studied tumorsample.

In the first stage of this analysis, called the Discovery Screen, theprimer pairs were used to amplify and sequence 175,471 coding exons andadjacent intronic splice donor and acceptor sequences in the 22 GBMsamples and in one matched normal sample. The data were assembled foreach amplified region and evaluated using stringent quality criteria,resulting in successful amplification and sequencing of 95.0% oftargeted amplicons and 93.0% of targeted bases in the 22 tumors. A totalof 689 Mb of sequence data were generated through this approach. Theamplicon traces were analyzed using automated approaches to identifychanges in the tumor sequences that were not present in the referencesequences of each gene, then alterations present in the normal controlsample and in single nucleotide polymorphism (SNP) databases wereremoved from further analyses. The remaining sequence traces ofpotential alterations were visually inspected to remove false-positivemutation calls generated through our automated software. All exonscontaining putative mutations were then re-amplified and sequenced inthe affected tumor and matched normal DNA samples. This process allowedconfirmation of the mutation in the tumor sample and determined whetherthe alteration was somatic (i.e. tumor-specific) or was present in thegermline. All putative somatic mutations were examined computationallyand experimentally to confirm that the alterations did not arise throughthe aberrant co-amplification of related gene sequences (12).

TABLE 1 Summary of genomic analyses of GBM Sequencing analysis Number ofgenes analyzed 20,583 Number of transcripts analyzed 23,781 Number ofexons analyzed 184,292 Primer pairs designed for amplification 219,229Fraction of passing amplicons* 95.0% Total number of nucleotidessequenced 689,071,123 Fraction of passing amplicon sequencessuccessfully 98.4% analyzed^(#) Fraction of targeted bases sucessfullyanalyzed^(#) 93.0% Number of somatic mutations identified (n = 22 2,328samples) Number of somatic mutations (excluding Br27P) 996 Missense 870Nonsense 43 Insertion 3 Deletion 46 Duplication 7 Splice site or UTR 27Average number of sequence alterations per sample 47.4 Copy numberanalysis Total number of SNP loci assessed for copy number 1,069,688changes Number of copy number alterations identified (n = 22 281samples) Amplifications 147 Homozygous deletions 134 Average number ofamplifications per sample 6.7 Average number of homozygous deletions persample 6.1 *Passing amplicons were defined as having PHRED20 scores orbetter over 90% of the target sequence in 75% of samples analyzed.^(#)Fraction of nucleotides having PHRED20 scores or better (seeSupporting Online Materials for additional information).

Example 7

Analysis of Sequence Alterations

We found that 2043 genes (10% of the 20,661 genes analyzed) contained atleast one somatic mutation that would be expected to alter the proteinsequence. The vast majority of these alterations were single-basesubstitutions (94%), while the others were small insertions, deletions,or duplications. The tumor sample Br27P obtained from the patientpreviously treated with radiation therapy and chemotherapy (includingtemozolomide), had 1332 total somatic mutations, 17-fold higher than anyof the other 21 patients (FIG. 10A, Table S3). The mutation spectrum ofthis sample, comprising an excess of C>T transitions in the 5′ cytosineof CpC dinucleotides, was dramatically different from those of the otherGBM patients, but was consistent with previous observations of ahypermutation phenotype in glioma samples of patients treated withtemozolomide (13, 14). In the previously-reported patients, thehypermutability was thought to occur due to prolonged exposure of anakylating agent in the presence of MSH6 mismatch repair deficiency;however, in BR27P, no somatic alterations were observed in MSH6 or inany of the other mismatch repair genes (MSH2, MLH1, MLH3, PMS 1, PMS2).In contrast to BR27P, none of the other 21 tumor samples analyzed in theDiscovery Screen were known to have received prior radiation orchemotherapeutic treatment, and none had the characteristic CpC mutationspectrum that has been found in such pre-treated tumors.

After removing Br27P from consideration, the remaining 993 mutationswere observed to be distributed relatively evenly among the 21 remainingtumors (FIG. 10A, Table S3). The number of somatic mutations identifiedin each tumor ranged between 17 and 79 with a mean of 47 mutations pertumor, or 1.51 mutations per Mb of GBM tumor genome sequenced. Six DNAsamples extracted from primary tumors had somewhat smaller numbers ofmutations than those obtained from xenografts, likely because of themasking effect of non-neoplastic cells in the former. It has previouslybeen shown that cell lines and xenografts provide the optimal templateDNA for cancer genome sequencing analyses (15) and that they faithfullyrepresent the alterations present in primary tumors (16).

Both the total number and frequency of sequence alterations in GBMs weresubstantially smaller than the number and frequency of such alterationsobserved in cancers of the colon or breast, and slightly less than inpancreas (10, 11, 17). The most likely explanation for this differenceis the reduced number of cell generations in glial cells prior to theonset of neoplasia. It has been suggested that up to half of the somaticmutations observed in colorectal cancers occur in epithelial stem cellsduring the normal cell renewal processes (16). As normal glial stemcells turn over much less frequently than mammary or colon epithelialcells, they would be expected to contain many fewer mutations when thetumor-initiating mutation occurred (18).

We further evaluated a set of 20 mutated genes identified in theDiscovery Screen in a second screen, called a Prevalence Screen,comprising an additional 83 GBMs with well-documented clinical histories(table S2, available on line at Science 26 Sep. 2008: Vol. 321. no.5897, pp. 1807-1812). These genes were mutated in at least two tumorsand had mutation frequencies >10 mutations per Mb of tumor DNAsequenced. Nonsilent somatic mutations were identified in 15 of these 20genes in the additional tumor samples (FIG. 10B, Table S4). The mutationfrequency of all analyzed genes in the Prevalence Screen was 24mutations per Mb of tumor DNA, markedly increased from the overallmutation frequency in the Discovery Screen of 1.5 mutations per Mb(p<0.001, binomial test). Additionally, the observed ratio of nonsilentto silent mutations (NS:S) among mutations in the Prevalence Screen was14.8:1, substantially higher than the 3.1:1 ratio that was observed inthe Discovery Screen (P<0.001, binomial test). The increased mutationfrequency and higher number of nonsilent mutations suggested that genesmutated in the Prevalence Screens were enriched for genes that activelycontributed to tumorigenesis.

In addition to the frequency of mutations in a gene, the type ofmutation can provide information useful for evaluating its potentialrole in disease (19). Nonsense mutations, out-of-frame insertions ordeletions, and splice site changes generally lead to inactivation of theprotein products. The likely effect of missense mutations can beassessed through evaluation of the mutated residue by evolutionary orstructural means. To evaluate missense mutations, we developed a newalgorithm that employs machine learning of 56 predictive features basedon the physical-chemical properties of amino acids involved in thesubstation and their evolutionary conservation at equivalent positionsof conserved proteins (12). Approximately 15% of the missense mutationsidentified in this study were predicted to have a statisticallysignificant effect on protein function when assessed by this method(FIG. 10A, Table S3). We were also able to make structural models of 244of the 870 missense mutations identified in this study (20). In eachcase, the model was based on x-ray crystallography or nuclear magneticresonance spectroscopy of the normal protein or a closely relatedhomolog. This analysis showed that 35 of the missense mutations werelocated close to a domain interface or substrate-binding site and werelikely to impact function (links to structural models available in(12)).

Example 8

Analysis of Copy Number Changes

The same tumors were then evaluated for copy number alterations throughgenomic hybridization of DNA samples to Illumina high densityoligonucleotide arrays containing ˜1 million SNP loci probes (21). Wehave recently developed a sensitive and specific approach for theidentification of focal amplifications resulting in 12 or more copiesper nucleus (6-fold or greater amplification compared to the diploidgenome) as well as deletions of both copies of a gene (homozygousdeletions) using such arrays (22). Such focused alterations can be usedto identify underlying candidate genes in these regions. It isimpossible to reliably identify such candidate genes in regions withlarger chromosomal aberrations, such as those involving gains or lossesof entire chromosomal arms, which occur frequently in tumors and are ofunknown significance.

We identified a total of 147 amplifications and 134 homozygous deletionsin the 22 samples used in the Discovery Screen, with 0 to 34amplifications and 0 to 14 deletions found per tumor sample. Althoughthe number of amplifications was similar between primary samples andthose tumors that had been passaged as xenografts, the latter samplesallowed detection of a larger number of homozygous deletions (average of8.0 deletions per xenograft versus 2.2 per primary sample). Theseobservations are consistent with previous reports documenting thedifficulty of identifying homozygous deletions in samples containingcontaminating normal DNA (23) and highlight the importance of usingpurified human tumor cells, such as those present in xenografts or celllines, for genomic analyses.

Example 9

Integration of Sequencing, Copy Number and Expression Analyses

Mutations that arise during tumorigenesis may provide a selectiveadvantage to the tumor cell (driver mutations) or have no net effect ontumor growth (passenger mutations). The mutational data obtained fromsequencing and analysis of copy number alterations were integrated inorder to identify GBM candidate cancer genes (CAN-genes) that would bemost likely to be drivers and therefore worthy of further investigation.The bioinformatic approach employed to determine if a gene was likely toharbor driver mutations involved comparison of the number and type ofmutations observed in each gene to the number that would be expected dueto the passenger mutation rates. For sequence alterations, we calculatedupper and lower bounds of passenger rates. The upper bound wasconservatively calculated as the total number of observed alterationsminus those mutations occurring in known cancer genes divided by theamount of tumor DNA sequenced, while the lower bound was determined onthe basis of the observed silent mutations and estimates of expectedNS:S ratios (12). For copy number changes, we made the very conservativeassumption that all amplifications and deletions were passengers whendetermining the background rate. For analysis of each gene, all types ofalterations (sequence changes, amplifications and homozygous deletions),were then combined to estimate the passenger probability for that gene(see (12) for a more detailed description of the statistical methods).

The top-ranked CAN-genes, together with their passenger probabilities,are listed in FIG. 10C, Table S7. The CAN-genes included a number ofgenes that had been well established with respect to their involvementin gliomas, including TP53, PTEN, CDKN2A, RB1, EGFR, NF1, PIK3CA andPIK3R1 (24-34). The most frequently altered of these genes in ouranalyses included CDKN2A (altered in 50% of GBMs), TP53, EGFR, and PTEN(altered in 30-40%), NF1, CDK4 and RB1 (altered in 12-15%), and PIK3CAand PIK3R1 (altered in 8-10%). Overall, these frequencies, which aresimilar to or in some cases higher than those previously reported,validate the sensitivity of our approach for detection of somaticalterations.

TABLE 2 Most frequently altered GBM CAN-genes Point mutations{circumflexover ( )} Amplifications^(&) Homozygous deletions^(&) Fraction of Numberof Fraction of Number of Fraction of Number of Fraction of tumors withPassenger Gene tumors tumors tumors tumors tumors tumors any alterationProbability* CDKN2A 0/22 0% 0/22 0% 11/22  50% 50% 0.00 TP53 37/105 35%0/22 0% 1/22 5% 40% 0.00 EGFR 15/105 14% 5/22 23% 0/22 0% 37% 0.00 PTEN27/105 26% 0/22 0% 1/22 5% 30% 0.00 NF1 16/105 15% 0/22 0% 0/22 0% 15%0.04 CDK4 0/22 0% 3/22 14% 0/22 0% 14% 0.00 RB1  8/105 8% 0/22 0% 1/225% 12% 0.01 IDH1 12/105 11% 0/22 0% 0/22 0% 11% 0.00 PIK3CA 10/105 10%0/22 0% 0/22 0% 10% 0.10 PIK3R1  8/105 8% 0/22 0% 0/22 0% 8% 0.14 Themost frequently-altered CAN-genes are listed; all CAN-genes are listedin Table S7. {circumflex over ( )}Fraction of tumors with pointmutations indicates the fraction of mutated GBMs out of the 105 samplesin the Discovery and Prevalence Screens. CDKN2A and CDK4 were notanalyzed for point mutations in the Prevalence Screen because nosequence alterations were detected in these genes in the DiscoveryScreen. ^(&)Fraction of tumors with amplifications and deletionsindicates the number of tumors with these types of alterations in the 22Discovery Screen samples. *Passenger probability indicates the Passengerprobability - Mid (12).

Analysis of additional gene members within pathways affected by thesegenes identified alterations of critical genes in the TP53 pathway(TP53, MDM2, MDM4), the RB1 pathway (RB1, CDK4, CDKN2A), and thePI3K/PTEN pathway (PIK3CA, PIK3R1, PTEN, IRS1). These alterationsresulted in aberrant pathways in a majority of tumors (64%, 68%, and50%, respectively) and in all cases but one, mutations within each tumoraffected only a single member of each pathway in a mutually exclusivemanner (P<0.05) (Table 3). Systematic analyses of functional gene groupsand pathways contained within the well-annotated MetaCore database (35)identified enrichment of mutated genes in additional members of the TP53and PI3K/PTEN pathways as well as in a variety of other cellularprocesses, including those regulating cell adhesion as well as brainspecific cellular pathways such those involving synaptic transmission,transmission of nerve impulses, and channels involved in transport ofsodium, potassium and calcium ions. Interestingly, none of these latterpathways were observed as being enriched in large-scale studies onpancreatic cancers (17) and may represent a subversion of normal glialcell processes to promote dysregulated growth and invasion. Many membersof the detected pathways had not been appreciated to have any role inGBMs or any other human cancer, and substantial effort will be requiredto determine their role in tumorigenesis.

TABLE 3 Mutations of the TP53, PI3K, and RB1 pathways in GBM samplesTP53 pathway PI3K Pathway RB1 pathway All All All Tumor sample TP53 MDM2MDM4 genes PTEN PIK3CA PIK3R1 IRS1 genes RB1 CDK4 CDKN2A genes Br02X DelAlt Mut Alt Del Alt Br03X Mut Alt Mut Alt Br04X Mut Alt Mut Alt Mut AltBr05X Amp Alt Mut Alt Del Alt Br06X Del Alt Br07X Mut Alt Mut Alt DelAlt Br08X Del Alt Br09P Mut Alt Amp Alt Br10P Mut Alt Br11P Mut AltBr12P Mut Alt Mut Alt Br13X Mut Alt Del Alt Br14X Mut Alt Del Alt Br15XMut Del Alt Br16X Amp Alt Amp Alt Br17X Mut Alt Del Alt Br20P Br23X MutAlt Del Alt Br25X Mut Alt Del Alt Br26X Mut Alt Del Alt Br27P Mut AltAmp Alt Br29P Mut Alt Fraction of tumors 0.55 0.05 0.05 0.64 0.27 0.090.09 0.05 0.50 0.14 0.14 0.45 0.68 with altered gene/pathway^(#) *Mut,mutated; Amp, amplified; Del, deleted; Alt, altered ^(#)Fraction ofaffected tumors in 22 Discovery Screen samples

Gene expression patterns can inform the analysis of pathways becausethey can reflect epigenetic alterations not detectable by sequencing orcopy number analyses. They can also point to downstream effects on geneexpression resulting from the altered pathways described above. Toanalyze the transcriptome of GBMs, we performed SAGE (serial analysis ofgene expression) (36) on all GBM samples used for mutation analysis forwhich RNA was available (total of 18 samples) as well as two independentnormal brain RNA controls. When combined with massively parallelsequencing-by-synthesis methods (37-40), SAGE provides a highlyquantitative and sensitive measure of gene expression.

The transcript analysis was first used to help identify target genesfrom the amplified and deleted regions that were identified in thisstudy. Though some of these regions contained a known tumor suppressorgene or oncogene, many contained several genes that had not previouslybeen implicated in cancer. A candidate target gene could be identifiedwithin several of these regions through the use of the mutational aswell as transcriptional data.

Second, we attempted to identify genes that were differentiallyexpressed in GBMs compared to normal brain. There was a high number(143) of genes that were expressed at an average 10-fold higher level in18 GBMs analyzed (compared to normal brain samples). Among the 143over-expressed genes, there were 16 that were secreted or expressed onthe cell surface. Many of these were over expressed in the xenografts aswell as in the primary brain tumors, suggesting new opportunities fordiagnostic and therapeutic applications.

Example 10

High Frequency Alterations of IDH 1 in Young GBM Patients

The top CAN-gene list (FIG. 10C, Table S7) included a number ofindividual genes which had not previously been linked to GBMs. The mostfrequently mutated of these genes, IDH1, encodes isocitratedehydrogenase 1, which catalyzes the oxidative carboxylation ofisocitrate to α-ketoglutarate, resulting in the production of NADPH.Five isocitrate dehydrogenase genes are encoded in the human genome,with the products of three (IDH3 alpha, IDH3 beta, IDH3 gamma) forming aheterotetramer (2 in the mitochondria and utilizing NAD(+) as anelectron acceptor to catalyze the rate-limiting step of thetricarboxylic acid cycle. The fourth isocitrate dehydrogenase (IDH2) isalso localized to the mitochondria, but like IDH1, uses NADP(+) as anelectron acceptor. The IDH1 product, unlike the rest of the IDHproteins, is contained within the cytoplasm and peroxisomes (41). Theprotein forms an asymmetric homodimer (42), and is thought to functionto regenerate NADPH and -ketoglutarate for intraperoxisomal andcytoplasmic biosynthetic processes. The production of cytoplasmic NADPHby IDH1 appears to play a significant role in cellular control ofoxidative damage (43) (44). None of the other IDH genes, other genesinvolved in the tricarboxylic acid cycle, or other peroxisomal proteinswere found to be genetically altered in our analysis.

IDH1 was found to be somatically mutated in five GBM tumors in theDiscovery Screen. Surprisingly, all five had the same heterozygous pointmutation, a change of a guanine to an adenine at position 395 of theIDH1 transcript (G395A), leading to a replacement of an arginine with ahistidine at amino acid residue 132 of the protein (R132H). In our priorstudy of colorectal cancers, this same codon had been found to bemutated in a single case through alteration of the adjacent nucleotide,resulting in a R132C amino acid change (10). Five additional GBMsevaluated in our Prevalence Screen were found to have heterozygous R132Hmutations, and an additional two tumors had a third distinct mutationaffecting the same amino acid residue, R132S (FIG. 1; Table 4). The R132residue is conserved in all known species and is localized to thesubstrate binding site, forming hydrophilic interaction with thealpha-carboxylate of isocitrate (FIG. 2) (42, 45).

TABLE 4 Characteristics of GBM patients with IDH1 mutations Patient ageRecurrent Secondary Overall survival IDH1 Mutation Mutation Mutation ofPTEN, Patient ID (years)* Sex GBM^(#) GBM{circumflex over ( )}(years)^(&) Nucleotide Amino acid of TP53 RB1, EGFR, or NF1 Br10P 30 FNo No 2.2 G395A R132H Yes No Br11P 32 M No No 4.1 G395A R132H Yes NoBr12P 31 M No No 1.6 G395A R132H Yes No Br104X 29 F No No 4.0 C394AR132S Yes No Br106X 36 M No No 3.8 G395A R132H Yes No Br122X 53 M No No7.8 G395A R132H No No Br123X 34 M No Yes 4.9 G395A R132H Yes No Br237T26 M No Yes 2.6 G395A R132H Yes No Br211T 28 F No Yes 0.3 G395A R132HYes No Br27P 32 M Yes Yes 1.2 G395A R132H Yes No Br129X 25 M Yes Yes 3.2C394A R132S No No Br29P 42 F Yes Unknown Unknown G395A R132H Yes No IDH133.2 67% M 25% 42% 3.8 100% 100% 83%  0% mutant patients (n = 12) IDH153.3 65% M 16%  1% 1.5  0%  0% 27% 60% wildtype patients (n = 93)*Patient age refers to age at which patient GBM sample was obtained.^(#)Recurrent GBM designates a GBM which was resected >3 months after aprior diagnosis of GBM. {circumflex over ( )}Secondary GBM designates aGBM which was resected >1 year after a prior diagnosis of a lower gradeglioma (WHO I-III). ^(&)Overall survival was calculated using date ofGBM diagnosis and date of death or last patient contact: patients Br10Pand Br11P were alive at last contact. Median survival for IDH1 mutantpatients and IDH1 wildtype patients was calculated using logrank test.Previous pathologic diagnoses in secondary GBM patients wereoligodendroglioma (WHO grade II) in Br123X, low grade glioma (WHO gradeI-II) in Br237T and Br211T, anaplastic astrocytoma (WHO grade III) inBr27P, and anaplastic oligodendroglioma (WHO grade III) in Br129X.Abbreviations: GBM (glioblastoma multiforme, WHO grade IV), WHO (WorldHealth Organization), M (male), F (female), mut (mutant). Mean age andmedian survival are listed for the groups of IDH1-mutated andIDH1-wildtype patients.

Several important observations were made about IDH1 mutations and theirpotential clinical significance. First, mutations in IDH1 preferentiallyoccurred in younger GBM patients, with a mean age of 33 years forIDH1-mutated patients, as opposed to 53 years for patients with wildtypeIDH1 (P<0.001, t-test, Table 4). In patients under 35 years of age,nearly 50% (9 of 19) had mutations in IDH1. Second, mutations in IDH1were found in nearly all of the patients with secondary GBMs (mutationsin 5 of 6 secondary GBM patients, as compared to 7 of 99 patients withprimary GBMs, P<0.001, binomial test), including all five secondary GBMpatients under 35 years of age. Third, patients with IDH1 mutations hada significantly improved prognosis, with a median overall survival of3.8 years as compared to 1.1 years for patients with wildtype IDH1(P<0.001, log-rank test). Although younger age and mutated TP53 areknown to be positive prognostic factors for GBM patients, thisassociation between IDH1 mutation and improved survival was noted evenin patients <45 years old (FIG. 3, P<0.001, log-rank test), as well asin the subgroup of young patients with TP53 mutations (P<0.02, log-ranktest).

REFERENCES AND NOTES

The disclosure of each reference cited is expressly incorporated herein.

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Example 11

Materials and Methods

Gene Selection

The protein coding exons from 23,781 transcripts representing 20,735unique genes were targeted for sequencing. This set comprised 14,554transcripts from the highly curated Consensus Coding Sequence (CCDS)database, a further 6,019 transcripts from the Reference Sequence(RefSeq) database, and an additional 3,208 transcripts with intact openreading frames from the Ensembl database, We excluded transcripts fromgenes that were located on the Y chromosome or were precisely duplicatedwithin the genome. As detailed below, 23,219 transcripts representing20,661 genes were successfully sequenced.

Bioinformatic Resources

Consensus Coding Sequence (Release 1), RefSeq (release 16, March 2006)and Ensembl (release 31) gene coordinates and sequences were acquiredfrom the UCSC Santa Cruz Genome Bioinformatics Site. The positionslisted in the Supplementary Tables correspond to UCSC Santa Cruz hg17,build 35.1. The single nucleotide polymorphisms used to filter-out knownSNPs were those present in dbSNP (release 125) that had been validatedby the HapMap project. BLAT and In Silico PCR were used to performhomology searches in the human and mouse genomes.

Primer Design

Primer 3 software was used to generate primers no closer than 50 bp tothe target boundaries, producing products of 300 to 600 bp. Exonsexceeding 350 bp were divided into several overlapping amplicons. Insilico PCR and BLAT were used to select primer pairs yielding a singlePCR product from a unique genomic position. Primer pairs for duplicatedregions giving multiple in silico PCR or BLAT hits were redesigned atpositions that were maximally different between the target andduplicated sequences. A universal primer (M13F, 5′-GTAAAACGACGGCCAGT-3′;SEQ ID NO: 136) was added to the 5′ end of the primer with the smallestnumber of mono- or dinucleotide repeats between itself and the targetregion. The primer sequences used in this study are listed in table S1available on line at Science 26 Sep. 2008: Vol. 321. no. 5897, pp.1807-1812.

Glioblastoma Multiforme (GBM) DNA Samples Tumor DNA was obtained fromGBM xenografts and primary tumors, with matched normal DNA for each caseobtained from peripheral blood samples, as previously described (1). TheDiscovery Screen consisted of 22 tumor samples (15 xenografts and 7primary tumors), with the Prevalence screen including another 83 samples(53 xenografts and 30 primary tumors). Additional clinical informationregarding Discovery and Prevalence Screen samples is available in tableS2, available on line at Science 26 Sep. 2008: Vol. 321. no. 5897, pp.1807-1812. All samples were given the histologic diagnosis ofglioblastoma multiforme (GBM; World Health Organization Grade IV),except for two Discovery Screen samples who were recorded as “high gradeglioma, not otherwise specified”. Samples were classified as recurrentfor patients in whom a GBM had been diagnosed at least 3 months prior tothe surgery when the study GBM sample was obtained. There were 3recurrent GBMs in the Discovery Screen, and 15 in the Prevalence Screen.Samples were classified as secondary for patients in whom a lower gradeglioma (WHO grade I-III) had been histologically confirmed at least 1year prior to the surgery when the study GBM sample was obtained. OneDiscovery Screen sample and 5 Prevalence Screen samples were classifiedas secondary.

TABLE 5 Overview of GBM samples used in the Prevalence and DiscoveryScreens: Discovery Validation Total Number of samples 22 83 105 Patientage Mean age (years) 48.6 51.7 51.0 Median age (years) 45 53 52 Patientsex Male 14 55 69 Female 8 28 36 Sample source Xenograft 15 53 68Primary tumor 7 30 37 GBM subclasses Recurrent 3 15 18 Recurrent withprior chemotherapy 1 10 11 Secondary 1 5 6

Pertinent clinical information, including date of birth, date study GBMsample obtained, date of original GBM diagnosis (if different than thedate that the GBM sample was obtained, as in the case of recurrentGBMs), date and pathology of preceding diagnosis of lower grade glioma(in cases of secondary GBMs), the administration of radiation therapyand/or chemotherapy prior to the date that the GBM sample was obtained,date of last patient contact, and patient status at last contact. Allsamples were obtained in accordance with the Health InsurancePortability and Accountability Act (HIPAA). All samples were obtained inaccordance with the Health Insurance Portability and Accountability Act(HIPAA). As previously described, tumor-normal pair matching wasconfirmed by typing nine STR loci using the PowerPlex 2.1 System(Promega, Madison, Wis.) and sample identities checked throughout theDiscovery and Prevalence screens by sequencing exon 3 of the HLA-A gene.PCR and sequencing was carried out as described in (1).

Statistical Analysis of Clinical Data

Paired normal and malignant tissue from 105 GBM patients were used forgenetic analysis. Complete clinical information (i.e. all pertinentclinical information such as date of initial GBM diagnosis, date ofdeath or last contact) was available for 91 of the 105 patients. Ofthese 91 patients, five (all IDH1-wildtype) died within the first monthafter surgery and were excluded from analysis (Br308T, Br246T, Br23X,Br301T, Br139X), as was a single patient (Br119X) with a presumedsurgical cure (also IDH1—wildtype) who was alive at last contact ˜10years after diagnosis. Kaplan Meier survival curves were compared usingthe Mantel Cox log-rank test. Hazard ratios were computed using theMantel-Haenszel method. The following definitions were used in the GBMpatient grouping and survival analysis computations: 1) Patient agereferred to the age at which the patient GBM sample was obtained. 2)Recurrent GBM designates a GBM which was resected >3 months after aprior diagnosis of GBM. 3) Secondary GBM designates a GBM which wasresected >1 year after a prior diagnosis of a lower grade glioma (WHO 4)Overall survival was calculated using date of GBM diagnosis and date ofdeath or last patient contact. All confidence intervals were calculatedat the 95% level.

Mutation Discovery Screen

CCDS, RefSeq and Ensembl genes were amplified in 22 GBM samples and onecontrol samples from normal tissues of one of the GBM patients. Allcoding sequences and the flanking 4 bp were analyzed using MutationsSurveyor (Softgenetics, State College, Pa.) coupled to a relationaldatabase (Microsoft SQL Server). For an amplicon to be further analyzed,at least three quarters of the tumors were required to have 90% or moreof bases in the region of interest with a Phred quality score of 20. Inthe amplicons that passed this quality control, mutations identical tothose observed in the normal sample as well as known single nucleotidepolymorphisms were removed. The sequencing chromatogram of each detectedmutation was then visually inspected to remove false positive calls bythe software. Every putative mutation was re-amplified and sequenced intumor DNA to eliminate artifacts. DNA from normal tissues of the samepatient in which the mutation was identified was amplified and sequencedto determine whether the mutations were somatic. When a mutation wasfound, BLAT was used to search the human and mouse genomes for relatedexons to ensure that putative mutations were the result of amplificationof homologous sequences. When there was a similar sequence with 90%identity over 90% of the target region, additional steps were performed.Mutations potentially arising from human duplications were re-amplifiedusing primers designed to distinguish between the two sequences.Mutations not observed using the new primer pair were excluded. Theremainder were included as long as the mutant base was not present inthe homologous sequence identified by BLAT. Mutations originallyobserved in mouse xenografts were re-amplified in DNA from primarytumors and included either if the mutation was present in the primarytumors or if the mutant was not identified in the homologous mousesequence identified by BLAT.

Mutation Prevalence Screen

We further evaluated a set of 20 mutated genes that had been identifiedin the Discover Screen in a second (Prevalence) screen, which includedan additional 83 GBMs (table S2). The genes selected were mutated in atleast two tumors and had mutation frequencies >10 mutations per Mb oftumor DNA sequenced. The primers used (table 51, available on line atScience 26 Sep. 2008: Vol. 321. no. 5897, pp. 1807-1812) and methods ofanalysis and duration of potential mutations were the same as in theDiscovery screen. All somatic mutations observed in the Prevalencescreen are reported in FIG. 10B, Table S4.

Copy Number Analysis

The Illumina Infinium II Whole Genome Genotyping Assay employing theBeadChip platform was used to analyze tumor samples at 1,072,820 (1M)SNP loci. All SNP positions were based on the hg18 (NCBI Build 36, March2006) version of the human genome reference sequence. The genotypingassay begins with hybridization to a 50 nucleotide oligo, followed by atwo-color fluorescent single base extension. Fluorescence intensityimage files were processed using Illumina BeadStation software toprovide normalized intensity values (R) for each SNP position. For eachSNP, the normalized experimental intensity value (R) was compared to theintensity values for that SNP from a training set of normal samples andrepresented as a ratio (called the “Log R Ratio”) of log2(Rexperimental/Rtraining set).

The SNP array data were analyzed using modifications of a previouslydescribed method (2). Homozygous deletions (HDs) were defined as threeor more consecutive SNPs with a Log R Ratio value of −2. The first andlast SNPs of the HD region were considered to be the boundaries of thealteration for subsequent analyses. To eliminate chip artifacts andpotential copy number polymorphisms, we removed all HDs that wereincluded in copy number polymorphism databases. Adjacent homozygousdeletions separated by three or fewer SNPs were considered to be part ofthe same deletion, as were HDs within 100,000 bp of each other. Toidentify the target genes affected by HDs, we compared the location ofcoding exons in the RefSeq, CCDS and Ensembl databases with the genomiccoordinates of the observed HDs. Any gene with a portion of its codingregion contained within a homozygous deletion was considered to beaffected by the deletion.

As outlined in (2), amplifications were defined by regions containingthree SNPs with an average Log R ratio 0.9, with at least one SNP havinga Log R ratio 1.4. As with HDs, we excluded all putative amplificationsthat had identical boundaries in multiple samples. As focalamplifications are more likely to be useful in identifying specifictarget genes, a second set of criteria were used to remove complexamplifications, large chromosomal regions or entire chromosomes thatshowed copy number gains. Amplifications >3 Mb in size and groups ofnearby amplifications (within 1 Mb) that were also >3 Mb in size wereconsidered complex. Amplifications or groups of amplifications thatoccurred at a frequency of 4 distinct amplifications in a 10 Mb regionor 5 amplifications per chromosome were deemed to be complex. Theamplifications remaining after these filtering steps were considered tobe focal amplifications and were the only ones included in subsequentstatistical analyses. To identify protein coding genes affected byamplifications, we compared the location of the start and stop positionsof each gene within the RefSeq, CCDS and Ensmbl databases with thegenomic coordinates of the observed amplifications. As amplificationscontaining only a fraction of a gene are less likely to have afunctional consequence, we only considered genes whose entire codingregions were included in the observed amplifications.

Estimation of Passenger Mutation Rates

From the synonymous mutations observed in the Discovery Screen, weestimated a lower bound of the passenger rate. The lower bound wasdefined as the product of the synonymous mutation rate and the NS:Sratio (1.02) observed in the HapMap database of human polymorphisms. Thecalculated rate of 0.38 mutations/Mb successfully sequenced is likely anunderestimate because selection against nonsynonymous mutations may bemore stringent in the germline than in somatic cells. An upper bound wascalculated from the total observed number of non-synonymous mutations/Mbafter excluding the most highly mutated genes known to be drivers fromprevious studies (TP53, PTEN, and RB1). The resultant passenger mutationrate of 1.02 non-synonymous mutations/Mb represents an over-estimate ofthe background rate as some of the mutations in genes other than TP53,PTEN, and RB1 were likely to be drivers. A ‘Mid” measure of 0.70mutations/Mb was obtained from the average of the lower and upper boundrates. For comparisons of the number and type of somatic mutationsidentified in the Discovery and Prevalence Screens, two sample t-testsbetween percents were used.

Expression Analysis

SAGE tags were generated using a Digital Gene Expression-Tag Profilingpreparation kit (Illumina, San Diego, Calif.) as recommended by themanufacturer. In brief, RNA was purified using guianidine isothiocyanateand reverse transcription with oligo-dT magnetic beads was performed on˜1 ug of total RNA from each sample. Second strand synthesis wasaccomplished through RNAse H nicking and DNA polymerase I extension. Thedouble-stranded cDNA was digested with the restriction enonuclease NlaIII and ligated to an adapter containing a Mme I restriction site. AfterMme I digestion, a second adapter was ligated, and the adapter-ligatedcDNA construct was enriched by 18 cycles of PCR and fragments of 85 bpwere purified from a polyacrylamide gel. The library size was estimatedusing real-time PCR and the tags sequenced on a Genome Analyzer System(Illumina, San Diego, Calif.).

Statistical Analysis

Overview of Statistical Analysis

The statistical analyses focused on quantifying the evidence that themutations in a gene or a biologically defined set of genes reflect anunderlying mutation rate that is higher than the passenger rate. In bothcases, the analysis integrates data on point mutations with data on copynumber alterations (CNA). The methodology for the analysis of pointmutations is based on that described in (3) while the methodology forintegration across point mutations and CNA's is based on (2). We providea self-contained summary herein, as several modifications to thepreviously described methods were required.

Statistical Analyses of CAN-Genes

The mutation profile of a gene refers to the number of each of thetwenty-five context-specific types of mutations defined earlier (3). Theevidence on mutation profiles is evaluated using an Empirical Bayesanalysis (4) comparing the experimental results to a referencedistribution representing a genome composed only of passenger genes.This is obtained by simulating mutations at the passenger rate in a waythat precisely replicates the experimental plan. Specifically, weconsider each gene in turn and simulate the number of mutations of eachtype from a binomial distribution with success probability equal to thecontext-specific passenger rate. The number of available nucleotides ineach context is the number of successfully sequenced nucleotides forthat particular context and gene in the samples studied. Whenconsidering nonsynonymous mutations other than indels, we focus onnucleotides at risk, as defined previously (3).

Using these simulated datasets, we evaluated the passenger probabilitiesfor each of the genes that were analyzed in this study. These passengerprobabilities represent statements about specific genes rather thanabout groups of genes. Each passenger probability is obtained via alogic related to that of likelihood ratios: the likelihood of observinga particular score in a gene if that gene is a passenger is compared tothe likelihood of observing it in the real data. The gene-specific scoreused in our analysis is based on the Likelihood Ratio Test (LRT) for thenull hypothesis that, for the gene under consideration, the mutationrate is the same as the passenger mutation rate. To obtain a score, wesimply transform the LRT to s=log(LRT). Higher scores indicate evidenceof mutation rates above the passenger rates. This general approach forevaluating passenger probabilities follows that described by Efron andTibshirani (4). Specifically, for any given score s, F(s) represents theproportion of simulated genes with scores higher than s in theexperimental data, F0 is the corresponding proportion in the simulateddata, and p0 is the estimated overall proportion of passenger genes(discussed below). The variation across simulations is small butnonetheless we generated and collated 100 datasets to estimate F0. Wethen numerically estimated the density functions f and f0 correspondingto F and F0 and calculated, for each score s, the ratio p0·f0(s)/f(s),also known as “local false discovery rate” (4). Density estimation wasperformed using the function “density” in the R statistical programminglanguage with default settings. The passenger probability calculationsdepend on an estimate of p0, the proportion of true passengers. Ourimplementation seeks to give an upper bound to p0 and thus provideconservatively high estimates of the passenger probability. To this endwe set p0=1. We also constrained the passenger probability to changemonotonically with the score by starting with the lowest values andrecursively setting values that decrease in the next value to theirright. We similarly constrain passenger probabilities to changemonotonically with the passenger rate.

An open source package for performing these calculations in the Rstatistical environment, named CancerMutationAnalysis, is available. Adetailed mathematical account of our specific implementation is providedin (5) and general analytic issues are discussed in (6).

Statistical Analysis of CNA. For each of the genes involved inamplifications or deletions, we further quantified the strength of theevidence that they drive tumorigenesis through stimations of theirpassenger probabilities. In each case, we obtain the passengerprobability as an a posteriori probability that integrates informationfrom the somatic mutation analysis of (3) with the data presented inthis article. The passenger probabilities derived from the pointmutation analysis serve as a priori probabilities. These are availablefor three different scenarios of passenger mutation rates and resultsare presented separately for each in FIG. 10A, Table S3. Then, alikelihood ratio for “driver” versus “passenger” was evaluated using asevidence the number of samples in which a gene was found to be amplified(or deleted). The passenger term is the probability that the gene inquestion is amplified (or deleted) at the frequency observed. For eachsample, we begin by computing the probability that the observedamplifications (and deletions) will include the gene in question bychance. Inclusion of all available SNPs is required for amplification,while any overlap of SNPs is sufficient for deletions. Specifically, ifin a specific sample N SNPs are typed, and K amplifications are found,whose sizes, in terms of SNPs involved, are A1 . . . AK, a gene with GSNPs will be included at random with probability (A 1−G+1)/N++(AK−G+1)/Nfor amplifications and (A 1+G−1)/N++(AK+G−1)/N for deletions. We thencompute the probability of the observed number of amplifications (ordeletions) assuming that the samples are independent but not identicallydistributed Bernoulli random variables, using the Thomas and Traubalgorithm (7). Our approach to evaluating the likelihood under the nullhypothesis is highly conservative, as it assumes that all the deletionsand amplifications observed only include passengers. The driver term ofthe likelihood ratio was approximated as for the passenger term, aftermultiplying the sample-specific passenger rates above by a gene-specificfactor reflecting the increase (alternative hypothesis) of interest.This increase is estimated by the ratio between the empirical deletionrate of the gene and the overall deletion rate.

This combination approach makes an approximating assumption ofindependence of amplifications and deletions. In reality, amplifiedgenes cannot be deleted, so independence is technically violated.However, because of the relatively small number of amplification anddeletion events, this assumption is tenable for the purposes of ouranalysis. Inspection of the likelihood, in a logarithmic scale, suggeststhat it is roughly linear in the overall number of events, supportingthe validity of this approximation as a scoring system.

Analysis of Mutated Gene Pathways and Groups

Four types of data were obtained from the MetaCore database (GeneGo,Inc., St. Joseph, Mich.): pathway maps, Gene Ontology (GO) processes,GeneGo process networks, and protein-protein interactions. Thememberships of each of the 23,781 transcripts in these categories wereretrieved from the databases using RefSeq identifiers. In GeneGo pathwaymaps, 22,622 relations were identified, involving 4,175 transcripts and509 pathways. For Gene Ontology processes, a total of 66,397 pairwiserelations were identified, involving 12,373 transcripts and 4,426 GOgroups. For GeneGo process networks, a total of 23,356 pairwiserelationships, involving 6,158 transcripts and 127 processes, wereidentified. The predicted protein products of each mutated gene werealso evaluated with respect to their physical interactions with proteinsencoded by other mutated genes as inferred from the MetaCore database.

For each of the gene sets considered, we quantified the strength of theevidence that they included a higher-than-average proportion of driversof carcinogenesis after consideration of set size. For this purpose, wesorted the genes by a score based on the combined passenger probabilitydescribed above (taking into account mutations, homozygous deletions,and amplifications). We compared the ranking of the genes contained inthe set with the ranking of those outside, using the Wilcoxon test, asimplemented by the Limma package in Bioconductor (8), then corrected formultiplicity by the q-value method with an alpha of 0.2 (9).

Bioinformatic Analysis

Overview of Bioinformatic Analysis

We have developed a novel bioinformatics software pipeline (depictedbelow) to compute: (1) a score for ranking somatic missense mutations bythe likelihood that they are passengers (LSMUT). The scores are based onproperties derived from protein sequences, amino acid residue changesand positions within the proteins; and (2) qualitative annotations ofeach mutation, based on protein structure homology models.

Mutation Scores

We tested several supervised machine learning algorithms to identify onethat would reliably distinguish between presumably neutral polymorphismsand cancer-associated mutations. The best algorithm was a Random Forest(12), which we trained on 2,840 cancer-associated mutations and 19,503polymorphisms from the SwissProt Variant Pages (13) using parallelRandom Forest software (PARF). Cancer-associated mutations wereidentified by parsing for the keywords “cancer”, “carcinoma”, “sarcoma”,“blastoma”, “melanoma”, “lymphoma”, “adenoma” and “glioma”. For eachmutation or polymorphism, we computed 58 numerical and categoricalfeatures (see table below). Two mutations present in the GBM tumorsamples were found in the SwissProt Variant Pages and removed from thetraining data. Because the training set contained ˜7 times as manypolymorphisms as cancer-associated mutations, we used class weights toupweight the minority class (cancer-associated mutation weight was 5.0and polymorphism weight was 1.0). The mtry parameter was set to 8 andthe forest size to 500 trees. Missing feature values were filled inusing the Random Forest proximity-based imputation algorithm (12) withsix iterations. Full parameter settings and all data used to build theRandom Forest are available upon request.

We then applied the trained forest to 594 GBM missense mutations and toa control set of 142 randomly generated missense mutations intranscripts of 78 genes that were found to be non-mutated in 11colorectal cancers (5). For each mutation, the 58 predictive featureswere computed as described above and the trained forest was used tocompute a predictive score for ranking the mutations. Specifically, thescores used are the fraction of trees that voted in favor of the“Polymorphic” class for each mutation.

To test the hypothesis that the scores of missense mutations intop-ranked CAN-genes were distributed differently than random missensemutations, we applied a modified Kolmogorov-Smirnov (KS) test, in whichties are broken by adding a very small random number to each score. Thescores of missense mutations in the top 13 CAN genes were found to besignificantly different from the mutations in the control set (P<0.001).

We estimate that mutations with scores <0.7 (˜15% of the missensemutations) are unlikely to be passengers. The threshold is based on theputative similarity of passengers to the neutral polymorphisms in theSwissProt Variant set, of which only ˜2% have scores <0.7. Scores ofSwissProt Variants were obtained by randomly partitioning them into twofolds, training a Random Forest on each (as described above) and thenscoring each fold with the Random Forest trained on the other one.

Homology Models

The protein translations of mRNA transcripts found to have somaticmissense mutations were input into ModPipe 1.0/MODELLER 9.1 homologymodel building software (14, 15). For each mutation, we identified allmodels that included the mutated position. If more than one model wasproduced for a mutation, we selected the model having the highestsequence identity with its template structure. The resulting model wasused to compute the solvent accessibility of the wild type residue atthe mutated position, using DSSP software (16). Accessibility valueswere normalized by dividing by the maximum residue solvent accessibilityfor each side chain type in a Gly-X-Gly tri-peptide (17). Solventaccessibilities greater than 36% were considered to be “exposed”, thosebetween 9% and 35% were considered “intermediate”, and those <9% wereconsidered “buried”. DSSP was also used to compute the secondarystructure of the mutated position. We used the LigBase (18) and PiBase(19) databases to identify mutated residue positions in the homologymodels that were close to ligands or domain interfaces in the equivalentpositions of their template structures. Finally, for each mutation, wegenerated an image of the mutation mapped onto its homology model withUCSF Chimera (20). The images and associated information for eachmutation are available. Model coordinates are available on request.

TABLE 6 The 58 numerical and categorical features used to train theRandom Forest # Feature Description 1 Net residue charge change Thechange in formal charge resulting from the mutation. 2 Net residuevolume change The change in residue volume resulting from the mutation(18). 3 Net residue hydrophobicity change The change in residuehydrophobicity resulting from the substitution (19). 4 Positional HiddenMarkov model This feature is calculated based on the degree ofconservation of (HMM) conservation score the residue estimated from amultiple sequence alignment built with SAM-T2K software (20), using theprotein in which the mutation occurred as the seed sequence (21). TheSAM-T2K alignments are large, superfamily-level alignments that includedistantly related homologs (as well as close homologs and orthologs) ofthe protein of interest. 5 Entropy of HMM alignment The Shannon entropycalculated for the column of the SAM- T2K multiple sequence alignment,corresponding to the location of the mutation (21). 6 Relative entropyof HMM alignment Difference in Shannon entropy calculated for the columnof the SAM-T2K multiple sequence alignment (corresponding to thelocation of the mutation) and that of a background distribution of aminoacid residues computed from a large sample of multiple sequencealignments (21). 7 Compatibility score for amino acid These multiplesequence alignments are calculated using groups substitution in thecolumn of a of orthologous proteins from the OMA database (22), whichare multiple sequence alignment of aligned with T-Coffee software (23).The compatibility score orthologs. for the mutation in the column ofinterest is computed as: (P(most frequent residue in the column) −2*P(wild type) + P(mutant) + P(Deletion) − 1)/(5 * number of uniqueamino acid residues in the column) 8 Grantham score The Granthamsubstitution score for the wild type => mutant transition (24).  9-11Predicted residue solvent accessibility These features consist of theprobability of the wild type residue being buried, intermediate orexposed as predicted by a neural network trained with Predict-2ndsoftware (20) on a set of 1763 proteins with high resolution X-raycrystal structures sharing less than 30% homology (25). 12-14 Predictedcontribution to protein These features consist of the probability thatthe wild type stability residue contributes to overall protein stabilityin a manner that is highly stabilizing, average or destabilizing, aspredicted by a neural network trained with Predict-2nd software (20) ona set of 1763 proteins with less than 30% homology. Stability estimatesfor the neural net training data were calculated using the FoldX forcefield (26). 15-17 Predicted flexibility (Bfactor) These features consistof the probability that the wild type residue backbone is stiff,intermediate or flexible as predicted by a neural network trained withPredict-2nd software (20) on a set of 1763 proteins with less than 30%homology. Flexibilities for the neural net training data were estimatedbased on normalized temperature factors, computed using the method of(27) from the X-ray crystal structure files. 18-20 Predicted secondarystructure These features consist of the probability that the secondarystructure of the region in which the wild type residue exists is helix,loop or strand as predicted by a neural net trained with Predict-2ndsoftware (20) on a set of 1763 proteins with crystal structures and withless than 30% homology. 21 Change in hydrophobicity Change in residuehydrophobicity due to the wild type → mutant transition. 22 Change involume Change in residue volume due to the wildtype → mutant transition.23 Change in charge Change in residue formal charge due to the wild type−> mutant transition. 24 Change in polarity Change in residue polaritydue to the wildtype → mutant transition. 25 EX substitution score Aminoacid substitution score from the EX matrix (28) 26 PAM250 substitutionscore Amino acid substitution score from the PAM250 matrix (29) 27BLOSUM 62 substitution score Amino acid substitution score from theBLOSUM 62 matrix (30) 28 MJ substitution score Amino acid substitutionscore from the Miyazawa-Jernigan contact energy matrix (28, 31) 29HGMD2003 mutation count Number of times that the wild type → mutantsubstitution occurs in the Human Gene Mutation Database, 2003 version(28, 32). 30 VB mutation count Amino acid substitution score from the VB(Venkatarajan and Braun) matrix (28, 33) 31-34 Probability of seeing thewild type Calculated by joint frequencies of amino acid triples in humanresidue in the first, middle, or last proteins found in UniProtKB (11)position of an amino acid triple 35-37 Probability of seeing the mutantCalculated by joint frequencies of amino acid triples in human residuein the first, middle, or last proteins found in UniProtKB (11) positionof an amino acid triple 38-40 Difference in probability of seeing theCalculated by joint frequencies of amino acid triples in human wildtypevs. the mutant residue in the proteins found in UniProtKB (11) first,middle, or last position of an amino acid triple 41 Probability ofseeing the wildtype at Calculated by a Markov chain of amino acidquintuples in the center of a window of 5 amino human proteins found inUniProtKB (11) acid residues 42 Probability of seeing the mutant at theCalculated by a Markov chain of amino acid quintuples in center of awindow of 5 amino acid human proteins found in UniProtKB (11) residues43-56 Binary categorical features from the These features giveannotations, curated from the literature, of UniProt KnowledgeBasefeature general binding sites, general active sites, lipid, metal, tablefor the protein product of the carbohydrate, DNA, phosphate and calciumbinding sites, transcript disulfides, seleno-cysteines, modifiedresidues, propeptide residues, signal peptide residues, known mutagenicsites, transmembrane regions, compositionally biased regions, repeatregions, known motifs, and zinc fingers. The integer 1 indicates that afeature is present and the integer 0 indicates that it is absent at amutated position.

REFERENCES FOR EXAMPLE 11

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The invention claimed is:
 1. A method of treating a mutant isocitratedehydrogenase 1 (IDH1) enzyme-associated central nervous system cancerin a subject comprising: detecting the presence of an isocitratedehydrogenase 1 (IDH1) mutation in a nucleic acid present in a sampleobtained from the subject, wherein the IDH1 mutation is present in amutant codon that corresponds to a wild type codon that encodes aminoacid 132 in the wild type IDH1 polypeptide of SEQ ID NO: 130; andadministering to the subject a chemotherapeutic agent to treat thecancer.
 2. The method of claim 1, wherein the mutant codon that includesthe IDH1 mutation encodes an amino acid selected from the groupconsisting of: histidine (H), cysteine (C), serine (S), leucine (L), andglycine (G).
 3. The method of claim 1, wherein the presence of an IDH1mutation in the sample is detected using an amplification primer, ahybridization probe, or both.
 4. The method of claim 3, wherein: theamplification primer comprises at least 10 but fewer than 600 contiguousnucleotide residues of a coding sequence of a IDH1 protein found in atumor of the subject, or its complement, the at least 10 contiguousnucleic acid residues comprising: a first nucleotide that is present ata position in a mutant codon that corresponds to a wild type codon thatencodes amino acid 132 in the wild type IDH1 polypeptide of SEQ ID NO:130, wherein the mutant codon comprising the first nucleotide encodes anamino acid selected from the group consisting of: histidine (H),cysteine (C), serine (S), leucine (L), and glycine (G), wherein theamplification primer is labeled with a detectable label; thehybridization probe comprises at least 10 but fewer than 600 contiguousnucleotide residues of a coding sequence of a IDH1 protein found in atumor of the subject, or its complement, the at least 10 contiguousnucleic acid residues comprising: a second nucleotide that is present ata position in a mutant codon that corresponds to a wild type codon thatencodes amino acid 132 in the wild type IDH1 polypeptide of SEQ ID NO:130, wherein the mutant codon comprising the second nucleotide encodesan amino acid selected from the group consisting of: histidine (H),cysteine (C), serine (S), leucine (L), and glycine (G), wherein thehybridization probe is labeled with a detectable label; or both.
 5. Themethod of claim 1, wherein the chemotherapeutic agent is a smallmolecule.
 6. The method of claim 1, wherein the IDH1 mutation results inthe subject expressing a mutant IDH1 polypeptide comprising an aminoacid substitution at position
 132. 7. The method of claim 6, wherein themutant IDH polypeptide comprises a R132C or a R132H amino acidsubstitution.
 8. A method of treating a mutant isocitrate dehydrogenase1 (IDH1) enzyme-associated central nervous system cancer in a subjectidentified as having an isocitrate dehydrogenase 1 (IDH1) mutation thatis present in a nucleic acid wherein the IDH1 mutation is present in amutant codon that encodes amino acid 132 in the wild type IDH1polypeptide of SEQ ID NO: 130, the method comprising: administering tothe subject a chemotherapeutic agent to treat the cancer.
 9. The methodof claim 8, wherein the mutant codon that includes the IDH1 mutationencodes an amino acid selected from the group consisting of: histidine(H), cysteine (C), serine (S), leucine (L), and glycine (G).
 10. Themethod of claim 8, wherein the subject is identified as having anisocitrate dehydrogenase 1 (IDH1) mutation by a method that employs anamplification primer, a hybridization probe, or both.
 11. The method ofclaim 10, wherein: the amplification primer comprises at least 10 butfewer than 600 contiguous nucleotide residues of a coding sequence of aIDH1 protein found in a tumor of the subject, or its complement, the atleast 10 contiguous nucleic acid residues comprising: a first nucleotidethat is present at a position in a mutant codon that corresponds to awild type codon that encodes amino acid 132 in the wild type IDH1polypeptide of SEQ ID NO: 130, wherein the mutant codon comprising thefirst nucleotide encodes an amino acid selected from the groupconsisting of: histidine (H), cysteine (C), serine (S), leucine (L), andglycine (G), wherein the amplification primer is labeled with adetectable label; the hybridization probe comprises at least 10 butfewer than 600 contiguous nucleotide residues of a coding sequence of aIDH1 protein found in a tumor of the subject, or its complement, the atleast 10 contiguous nucleic acid residues comprising: a secondnucleotide that is present at a position in a mutant codon thatcorresponds to a wild type codon that encodes amino acid 132 in the wildtype IDH1 polypeptide of SEQ ID NO: 130, wherein the mutant codoncomprising the second nucleotide encodes an amino acid selected from thegroup consisting of: histidine (H), cysteine (C), serine (S), leucine(L), and glycine (G), wherein the hybridization probe is labeled with adetectable label; or both.
 12. The method of claim 8, wherein thechemotherapeutic agent is a small molecule.
 13. The method of claim 8,wherein the IDH1 mutation results in the subject expressing a mutantIDH1 polypeptide comprising an amino acid substitution at position 132.14. The method of claim 13, wherein the mutant IDH polypeptide comprisesa R132C or a R132H amino acid substitution.
 15. A method of treating amutant isocitrate dehydrogenase 1 (IDH1) enzyme-associated centralnervous system cancer in a subject identified as having an isocitratedehydrogenase 1 (IDH1) mutation that is present in a nucleic acid,wherein the IDH1 mutation results in the subject expressing an IDH1polypeptide comprising a R132C or a R132H amino acid substitution, themethod comprising: administering to the subject a small moleculechemotherapeutic agent to treat the cancer.
 16. The method of claim 15,wherein the subject is identified as having an isocitrate dehydrogenase1 (IDH1) mutation by a method that employs an amplification primer,wherein the amplification primer comprises at least 10 but fewer than600 contiguous nucleotide residues of a coding sequence of a IDH1protein found in a tumor of the subject, or its complement, the at least10 contiguous nucleic acid residues comprising: a first nucleotide thatis present at a position in a mutant codon that corresponds to a wildtype codon that encodes amino acid 132 in the wild type IDH1 polypeptideof SEQ ID NO: 130, wherein the mutant codon comprising the firstnucleotide encodes an amino acid selected from the group consisting of:histidine (H), cysteine (C), serine (S), leucine (L), and glycine (G),wherein the amplification primer is labeled with a detectable label; orwherein the subject is identified as having an isocitrate dehydrogenase1 (IDH1) mutation by a method that employs a hybridization probe,wherein the hybridization probe comprises at least 10 but fewer than 600contiguous nucleotide residues of a coding sequence of a IDH1 proteinfound in a tumor of the subject, or its complement, the at least 10contiguous nucleic acid residues comprising: a second nucleotide that ispresent at a position in a mutant codon that corresponds to a wild typecodon that encodes amino acid 132 in the wild type IDH1 polypeptide ofSEQ ID NO: 130, wherein the mutant codon comprising the secondnucleotide encodes an amino acid selected from the group consisting of:histidine (H), cysteine (C), serine (S), leucine (L), and glycine (G),wherein the hybridization probe is labeled with a detectable label; orboth.